Compositions and methods for making and using hydrolytic enzymes for degrading polysaccharides made by foodborne pathogenic bacteria

ABSTRACT

Compositions and uses involving L. monocytogenes PssZ, as well as homologs, variants, and fragments thereof, are described.

RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.15/522,949, a National Stage Application of PCT/US2015/058038, filedOct. 29, 2015, and claims the benefit of U.S. Provisional ApplicationNo. 62/072,358, filed under 35 U.S.C. § 111(b) on Oct. 29, 2014, thedisclosure of each of which are incorporated herein by reference in theentirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Hatch Grantproject number WYO-491-13 awarded by the U.S. Department of Agriculture,National Institute of Food and Agriculture; and grant number MCB1052575awarded by the National Science Foundation. The government has certainrights in this invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Oct. 29, 2015, isnamed 53-56551_15-027_SL.txt and is 57,439 bytes in size.

BACKGROUND OF THE INVENTION

Bacteria can form exopolysaccharide-rich aggregates, or biofilms, thatpose formidable challenges in medicine and industry because of theirresistance to antibiotics, disinfectants, desiccation, and othertreatments. One of the common foodborne pathogens, Listeriamonocytogenes, can form biofilms on food products, food-processingequipment, and in food storage facilities. When consumed with food, L.monocytogenes may cause listeriosis, a severe disease that has thehighest fatality rate of the foodborne diseases in the developedcountries. Listeriosis is particularly dangerous for immunocompromisedindividuals, pregnant women, the elderly, and infants. Despite arelatively low number of cases, it is the third most costly foodbornedisease in the USA, with the total annual financial loss estimated at$8.8 billion. Thus, there is a need for new and improved means fordegrading biofilms and combating L. monocytogenes.

SUMMARY OF THE INVENTION

Described are uses of a Listeria monocytogenes PssZ protein, homolog,variant, or fragment, in preventing bacterialexopolysaccharide-dependent aggregation, in degrading a biofilm, and ininhibiting biofilm formation on a surface.

Provided is a L. monocytogenes PssZ protein having the sequence:

[SEQ ID NO: 1] MKRFILILILLIFIGAGFFIFLRPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHFFDYINKEITLKK.

Also provided are PssZ variants comprising 90%, 80%, 70%, or 60%sequence identity to the purified L. monocytogenes PssZ protein. Alsoprovided is a PssZ E72Q mutant comprising an L. monocytogenes PssZprotein having a Glu72 site substituted with glutamine.

Also provided is a purified PssZ fragment having the sequence:

[SEQ ID NO: 2] RPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHF FDYINKEITLKK.

Also provided are homologs of the L. monocytogenes PssZ protein. Incertain embodiments, the PssZ homolog is selected from the groupconsisting of: Exiguobacterium undae PssZ [SEQ ID NO: 47],Carnobacterium mobile PssZ [SEQ ID NO: 50], Carnobacterium jeotgali PssZ[SEQ ID NO: 53], Jeotgalibacillus campisalis PssZ [SEQ ID NO: 56], andBacillus thermotolerans PssZ [SEQ ID NO: 59].

Also provided is the use of a purified L. monocytogenes PssZ protein, aPssZ protein homolog, or a variant or fragment thereof, in hydrolyzing alisterial exopolysaccharide, or in preventing bacterialexopolysaccharide-dependent aggregation.

Further provided is a method of hydrolyzing a listerialexopolysaccharide, where the method involves exposing listeria bacteriato a sufficient amount of a purified L. monocytogenes PssZ protein, aPssZ protein homolog, or a variant or fragment thereof, and hydrolyzinga listerial exopolysaccharide. In certain embodiments, the listerialexopolysaccharide comprises ManNAc-Gal Pss exopolysaccharide. In certainembodiments, the listeria bacteria is present in a food article.

Further provided is a method of preventing bacterialexopolysaccharide-dependent aggregation on a surface, where the methodinvolves applying a sufficient amount of a purified L. monocytogenesPssZ protein, a PssZ protein homolog, or variant or fragment thereof, toa surface, and preventing bacterial exopolysaccharide-dependentaggregation on the surface. In certain embodiments, aggregation of L.monocytogenes is prevented. In certain embodiments, the surfacecomprises a food container surface. In certain embodiments, the surfacecomprises surface of fruit, vegetables, or other plant materials.

Further provided is a method of disintegrating bacterialexopolysaccharide-rich aggregates, where the method involves applying asufficient amount of a purified L. monocytogenes PssZ protein, a PssZprotein homolog, or a variant or fragment thereof, to a bacterialaggregate, and disintegrating the bacterial aggregate.

Further provided is a method of inhibiting a listerial contamination ina food article, where the method involves applying a sufficient amountof a purified L. monocytogenes PssZ protein, a PssZ protein homolog, ora variant or fragment thereof, to a food article, and inhibiting alisterial growth in the food article.

Further provided is a method of ameliorating a listerial contaminationin a food article, where the method involves applying a sufficientamount of a purified L. monocytogenes PssZ protein, a PssZ proteinhomolog, or a variant or fragment thereof, to a food articlecontaminated with L. monocytogenes, and applying a sufficient amount ofan antibacterial agent to the food article, to ameliorate the listerialcontamination in the food article. In certain embodiments, theantibacterial agent is bleach (sodium hypochlorite), hydrogen peroxide,or another disinfectant.

Further provided is a disinfecting solution that includes a PssZprotein, a PssZ protein homolog, or a variant or fragment thereof, andan antibacterial agent. In certain embodiments, the antibacterial agentis a detergent. In certain embodiments, the antibacterial agent isbleach. In certain embodiments, the antibacterial agent is selected fromthe group consisting of: hydrogen peroxide, alcohol, iodophor,quaternary ammonia compounds, chlorine solutions, peracetic acid,peroctanoic acid, nitric acid, benzoic acid, sodium hydroxide, dimethylbenzyl lauryl ammonium bromide, cationic surfactants, anionicsurfactants, non-ionic surfactants, zwitterionic surfactants, nisin,lauricidin, lactoperoxidase, ampicillin, vancomycin, ciprofloxacin,azithromycin, or a proteolytic enzyme. In certain embodiments, thedisinfecting solution has a pH ranging from about 4 to about 10.

Further provided is a polysaccharide composition that includes aManNAc-Gal exopolysaccharide (EPS) having a trisaccharide repeating unitof {4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, wherein ManpNAc isN-acetylmannosamine and Galp is galactose. In certain embodiments, thecomposition is a food additive or filler.

Further provided is a method of administering a probiotic, where themethod involves protecting a therapeutically effective amount of amicroorganism with an EPS coating to form a protected probiotic, andadministering the protected probiotic to a patient in need thereof.

Further provided is a kit for treating a bacterial contamination, wherethe kit includes a first container housing a PssZ enzyme solution, and asecond container housing a disinfectant solution. In certainembodiments, the PssZ enzyme solution comprises a PssZ protein, a PssZprotein homolog, or a variant or fragment thereof.

In certain embodiments, the PssZ protein homolog is selected from thegroup consisting of: Exiguobacterium undae PssZ [SEQ ID NO: 47],Carnobacterium mobile PssZ [SEQ ID NO: 50], Carnobacterium jeotgali PssZ[SEQ ID NO: 53], Jeotgalibacillus campisalis PssZ [SEQ ID NO: 56], andBacillus thermotolerans PssZ [SEQ ID NO: 59].

In certain embodiments, the fragment is a PssZ fragment having thesequence:

[SEQ ID NO: 2] RPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHF FDYINKEITLKK.

In certain embodiments, the PssZ variants comprise 90%, 80%, 70%, or 60%sequence identity to the purified L. monocytogenes PssZ protein.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file may contain one or more drawings executedin color and/or one or more photographs. Copies of this patent or patentapplication publication with color drawing(s) and/or photograph(s) willbe provided by the U.S. Patent and Trademark Office upon request andpayment of the necessary fees.

FIG. 1: In silico analysis of genes and proteins involved in c-di-GMPsignaling in L. monocytogenes. Depicted are genes believed to encodeDGCs (DgcA-C), c-di-GMP PDEs (PdeB-D), a c-di-GMP receptor (PssE), andlisterial EPS biosynthesis machinery. Protein domain architectures aretaken from the Pfam database: 5TM, a conserved five-transmembranemodule; unmarked red box, transmembrane domain; crossed GGDEF domain(“GGDEF” disclosed as SEQ ID NO: 3), enzymatically inactive GGDEF domain(“GGDEF” disclosed as SEQ ID NO: 3).

FIGS. 2A-2C: PDE activities of the L. monocytogenes proteins PdeBD. FIG.2A shows restoration of motility in semi-solid (0.25%) agar of strainMG1655 DyhjH by L. monocytogenes PdeB, PdeC, and PdeD is indicative oftheir cdi-GMP PDE activities. PdeB-D were expressed as C-terminalHis₆-fusions (“His₆” disclosed as SEQ ID NO: 4) downstream of the T7promoter from vector pET23a. Although MG1655 does not encode a T7 RNApolymerase gene, the pde genes were expressed from a fortuitous promoterat sufficiently high levels to partially restore the swimming defect ofMG1655 DyhjH in semi-solid agar. pET, empty vector (pET23a). FIG. 2Bshows affinity purified L. monocytogenes PdeD (PdeD::His₆) (“His₆”disclosed as SEQ ID NO: 4), PdeB (PdeB::His₆) (“His₆” disclosed as SEQID NO: 4), and PdeC (MBP::PdeC) proteins used in the PDE assays. MW,molecular weight, kD. FIG. 2C shows PDE activities of PdeD::His6 (“His6”disclosed as SEQ ID NO: 4), PdeB::His6 (“His6” disclosed as SEQ ID NO:4) and MBP::PdeC monitored by the rates of formation of pGpG, theproduct of c-di-GMP hydrolysis. Nucleotides were measured by HPLC asdescribed in the examples.

FIGS. 3A-3B: DGC activities of the L. monocytogenes proteins DgcAC. FIG.3A shows inhibition of motility in semi-solid (0.25%) agar of strainMG1655 by L. monocytogenes DgcA (plasmid pBAD-dgcA), DgcB (pBAD-dgcB),and DgcC (pBAD-dgcC) is indicative of their DGC activities. DgcA-C wereexpressed from the vector pBAD/Myc-His-C (pBAD). LB agar contained 0.1%arabinose. FIG. 3B shows Congo red staining of the fimbriae producingstrain BL21(DE3) caused by L. monocytogenes DgcA, DgcB, and DgcC isindicative of their DGC activities. LB agar contained 0.001% arabinose.

FIGS. 4A-4E: Inhibition of motility and activation of EPS production inL. monocytogenes by elevated levels of c-di-GMP. FIG. 4A, top, showsinhibition of swimming of the wild-type L. monocytogenes in semi-solidagar by a heterologous DGC, Slr1143. FIG. 4A, bottom, shows restorationof swimming in semi-solid agar of the L. monocytogenes ΔpdeB/C/D mutantby a heterologous PDE, YhjH. WT, wild type, EGD-e; A/B/C, ΔpdeB/C/Dmutant; pIMK, WT::pIMK2 (vector control); slr, WT::(pIMK2::slr1143);yhjH, WT::(pIMK2::yhjH). FIG. 4B shows Congo red staining of EPS in L.monocytogenes. 1, WT, wild type; 2, ΔpdeB/C/D; 3, ΔpdeB/C/D ΔpssE; 4,ΔpdeB/C/D ΔpssC; 5, ΔpdeB/C/D::pIMK2; 6, ΔpdeB/C/D::pIMK2::yhjH; 7,ΔpdeB/C/D::(pIMK2::slr1143); 8, WT::pIMK2; 9, WT::(pIMK2::yhjH); 10,WT::(pIMK2::slr1143). FIG. 4C shows deletion of all three c-di-GMP PDEsdrastically inhibits motility of L. monocytogenes in semi-solid agar.WT, wild type strain, B, ΔpdeB; C, ΔpdeC; D, ΔpdeD; B/D, ΔpdeB ΔpdeD;C/D, ΔpdeC ΔpdeD; B/C, ΔpdeB ΔpdeC; B/C/D, ΔpdeB/C/D. FIG. 4D showsrough colony morphology and increased Congo red staining of the L.monocytogenes ΔpdeB/C/D mutant and rescue of the wild-type colonymorphology by the ΔpssC mutation (ΔpdeB/C/D ΔpssC). FIG. 4E showsrestoration of motility of the ΔpdeB/C/D mutant by the ΔpssC or ΔpssEmutations.

FIGS. 5A-5B: In vitro assay of c-di-GMP binding by the PssE receptor.FIG. 5A shows the MBP-PssE protein purified via affinity (amylose resin)chromatography. The GGDEF domain of PssE (residues 107-285) (“GGDEF”disclosed as SEQ ID NO: 3) containing the putative I-site was fuseddownstream of MBP, MBP::GGDEFpssE (“GGDEF” disclosed as SEQ ID NO: 3),and used in c-di-GMP binding assays. FIG. 5B shows a saturation plot ofequilibrium binding of c-di-GMP to the PssE receptor (MBP::GGDEFpssE)(“GGDEF” disclosed as SEQ ID NO: 3). Shown is the dependence of theratio of bound cdi-GMP per protein in the dialysis chamber, whereprotein alone was loaded, versus concentration of free c-di-GMP atequilibrium.

FIGS. 6A-6D: Role of the c-di-GMP-induced EPS in biofilm formation, cellaggregation, and tolerance of L. monocytogenes to disinfectants anddesiccation. FIG. 6A shows biofilm formation of L. monocytogenes in96-well polystyrene plates (measured using a Crystal violet dyebindingassay). Cultures were grown for 6 days at 30° C. in LB (top panel) or LBsupplemented with 3% glycerol (bottom panel). Shown are average resultsfrom two biological replicates, where each strain was grown in six wellsin a replicate (i.e., six technical replicates). Black circle, wildtype; red square, ΔpdeB/C/D; green triangle, ΔpdeB/C/D ΔpssC; bluecross, ΔpdeB/C/D ΔpssE. FIG. 6B shows EPS-dependent L. monocytogenescell aggregation (clumping) in HTM medium. Overnight cultures grown inBHI were inoculated into HTM liquid medium at A600 of 0.01 and incubatedat 30° C. with gentle shaking (rotary shaker, 125 rpm) for 48 h. 1,ΔpdeB/C/D; 2, wild type; 3, ΔpdeB/C/D DpssC; 4, ΔpdeB/C/D ΔpssE. FIG. 6Cshows the protective role of the c-di-GMP-inducible EPS in disinfection.Aliquots of the HTM-grown cultures were mixed with disinfectantsolutions for 10 min at room temperature. Disinfection was stopped byadding a D/E neutralizing broth (Difco); the cultures were vortexedvigorously (5 min) with glass beads to break clumps and plated on BHIagar. Colonies were enumerated after a 48-h growth at 37° C. SH, sodiumhydrochloride (1600 ppm); HP, hydrogen peroxide (200 mM); BC,benzalkonium chloride (100 ppm). White background, EGD-e; black,ΔpdeB/C/D; grey, ΔpdeB/C/D ΔpssC. SH, sodium hypochlorite; HP, hydrogenperoxide; BC, benzalkonium chloride. The absence of the bar for theEGD-e strain treated with SH indicates the lack of survivors. FIG. 6Dshows the protective role of the c-di-GMP inducible EPS in desiccation.Aliquots of overnight cultures grown in HTM at 37° C. were spun down,the supernatants were removed, and cell pellets were stored indesiccators at room temperature for the indicated periods. The pelletswere rehydrated, vortexed with glass beads for better suspension andplated on BHI agar. The numbers of surviving colonies after incubationat 37° C. for 24 h are plotted. In FIGS. 6C-6D, the bars denote meanvalues for data from three biological replicates. *, significantlydifferent (p,0.002), **, significantly different (p,0.02), according toTukey test (Minitab 16 statistical software).

FIGS. 7A-7B: Impaired invasion of L. monocytogenes in HT-29 human colonadenocarcinoma cells by elevated c-di-GMP levels. FIG. 7A showsexpression of the heterologous DGC, Slr1143 (WT::slr; blue bar), ordeletion of the native PDEs (ΔpdeB/C/D; black), strongly inhibitlisterial invasion, compared to EGD-e containing an empty vector(WT::pIMK; white), while overexpression of the heterologous PDE, YhjH(WT::yhjH; yellow), improves invasion. FIG. 7B shows high intracellularc-di-GMP levels inhibit invasion more significantly than the presence ofEPS. Strains shown are WT (white bar); ΔpdeB/C/D mutant (black);ΔpdeB/C/D ΔpssC (dark-grey), and ΔpdeB/C/D ΔpssE (light-grey). Plottedare values of relative invasion, compared to those of WT::pIMK (FIG. 7A)or WT (FIG. 7B). Average results from three independent tests, eachperformed in three replicates are shown. *, significantly different(p,0.001). Prism 5 for Mac (GraphPad) was used to perform unpairedStudent's t-tests.

FIG. 8: Impaired spreading of the L. monocytogenes ΔpdeB/C/D mutant tothe liver and gallbladder in a foodborne model of infection. Groups ofBALB/c/By/J mice were fed 5.9-7.5×10⁸ CFU of the indicated L.monocytogenes strains and bacterial loads were assessed 60 hpost-infection. Dashed lines indicate the limit of detection for eachtissue. Bars denote mean values for pooled data from three separateexperiments. **, significantly different (p,0.05). Prism 5 for Mac(GraphPad) was used to perform unpaired Student's t-tests.

FIGS. 9A-9C: Cell aggregation in HTM/G medium and scanning electronmicroscopy (SEM) images of corresponding cultures. Top row in FIG. 9A:the EPS overproducing ΔpdeB/C/D strain grows in clumps in HTM/G mediumat 30° C. after 48 h whereas the wilde-type (EGD-e) and ΔpdeB/C/D ΔpssCstrains are not aggregated. Bottom row in FIG. 9A: SEM images of thecultures from the top row. FIGS. 9B-9C show SEM images of cell-boundintercellular adhesive listerial ManNAc-Gal EPS. These images were takenfrom the same culture of the ΔpdeB/C/D strain shown in FIG. 9A.

FIGS. 10A-10C: Phenotypic analysis of mutants in EPS biosynthesis. FIG.10A shows a map of the pssA-E operon (lmo0527-lmo0531). FIG. 10B shows aCongo red binding assay of the ΔpdeB/C/D strain containing deletions inthe pss operon. Cells were grown on HTM/G agar supplemented with 40 μgmL-1 Congo red dye at 30° C. for 48 h. FIG. 10C shows a cell aggregationassay of the ΔpdeB/C/D strain containing deletions in the pss operon.Cells were grown in HTM/G liquid medium at 30° C. for 48 h. Straindesignation in FIGS. 10B and 10C: 1, EGD-e; 2, ΔpdeB/C/D; 3, ΔpdeB/C/DΔpssE; 4, ΔpdeB/C/D ΔpssD; 5, ΔpdeB/C/D ΔpssC; 6, ΔpdeB/C/D ΔpssB; 7,ΔpdeB/C/D ΔpssA.

FIGS. 11A-11C: Phylogenetic tree analysis of proteins involved inlisterial ManNAc-Gal EPS biosynthesis. FIG. 11A shows a phylogenetictree constructed with L. monocytogenes PssC and glycosyl transferasefamily 2-3 proteins (seed alignment in Pfam). FIG. 11B shows aphylogenetic tree constructed with L. monocytogenes PssD and BcsB domainproteins. FIG. 11C shows a phylogenetic tree constructed with L.monocytogenes PssZ and glycosyl hydrolase family 8 (GH8) proteins.

FIG. 12: Repeating unit structure of listerial ManNAc-Gal EPS. Shown isa polymer of β1-4 linked ManNAc residues containing Gal branchesattached via an α or β configuration.

FIGS. 13A-13C: Structural analysis of listerial ManNAc-Gal EPS. FIG. 13Ashows the 1-D proton NMR spectrum of EPS-N (bottom) and EPS-H (top). TheManN anomeric signal in EPS-N appears smaller than the Gal anomericsignal. This is because it has significantly greater linewidth, as shownin the inset. Deconvolution and integration of the two signals showsthat the intensity of the ManN peak is about twice that of the Gal peak.Blue lines are the fitted peaks, the green line is the sum curve, andthe red line is the residue curve. FIG. 13B shows a multiplicity-edited2D ₁H-₁₃C—HSQC NMR spectra of EPS-N (left) and EPS-H (right).Multiplicity-editing causes signals from methyl and methane groups to bepositive (red) and signals from methylene groups to be negative (blue).FIG. 13C shows a portion of the NOESY spectra of EPS-N (left) and EPS-H(right). Labeling in all panels refers to Table 2.

FIG. 14: Anomeric region of the HSQC spetra. Top: EPS-H. Bottom:mannosamine hydrochloride. HSQC spectra were obtained without decouplingduring acquisition for the measurements of one-bond C—H couplingconstants.

FIGS. 15A-15D: Structures of secreted L. monocytogenes carbohydrates.FIG. 15A shows 1D ¹H-NMR spetra of the soluble carbohydrate preparationsfrom the ΔpdeB/C/D and ΔpdeB/C/D ΔpssC strains compared to those of purestandard samples of N-acetyl-D-glucosamine and rhamnose. These spectrashow how the peak patterns of the standard samples fit well with thoseof the strain samples. FIG. 15B shows a 2D ¹H-TOCSY spectrum at 298 K(5.10-3.30 ppm region) of the soluble carbohydrate prep from theΔpdeB/C/D strain showing the assignments for sugar protons. The signalsat 5.00 and 4.90 ppm are assigned to the anomeric protons (H1 and H1′)of N-acetylglucosamine and rhamnose, respectively. The signals ofprotons 2/2′, 3/3′, and 5′/5′ overlap for both sugar molecules due tothe similarities in their chemical structures. FIG. 15C shows a 2D¹H-TOCSY spectrum of the soluble carbohydrate prep from the ΔpdeB/C/Dstrain in H₂O at 298 K displaying the connectivities of the NH proton inN-acetylglucosamine. FIG. 15D shows a 2D ¹H-TOCSY spectrum of thesoluble carbohydrate prep from the ΔpdeB/C/D strain in D₂O at 298 Kindicating the presence of the CH₃ groups in N-acetylglucosamine andrhamnose. The CH₃ protons in rhamnose (C′H₃) exhibit severalcross-connectivities with the body of this sugar. On the other hand, theCH₃ group protons in N-acetylglucosamine show no connectivities due toits attachment to a quarternary carbon atom.

FIGS. 16A-16D: Phenotypic analysis of mutants in EPS degradation. FIG.16A shows a map of the dgcA-dgcB-pssZ-pdeC (lmo1911-lmo1914) genecluster. FIG. 16B shows a Congo red binding assay of strains withdeleted or overexpressed pssZ genes. FIG. 16C shows a cell aggregationassay of strains with deleted or overexpressed pssZ genes. Straindesignation in FIGS. 16B-16C: 1, ΔpdeB/C/D; 2, ΔpdeB/C/D ΔpssZ; 3,ΔpdeB/C/D ΔpssZ pIMK2-pssZ; 4, ΔpdeB/C/D ΔpssZ pIMK2-pssZ E72Q; 5,ΔpdeB/C/D pIMK2-pssZ; 6, EGD-e; 7, ΔpdeB/C/D ΔpssC. Note that onlystrains 1-5 were analyzed in FIG. 16C. FIG. 16D shows aggregation ofstrains with deleted or overexpressed pssZ genes assessed by drop inoptical density. The drop in the optical density correlates with thedegree of cell aggregation. Data are derived from two independentbiological repeats each with three measurements. Note that the red andpurple lines are superimposed.

FIGS. 17A-17D: ManNAc-Gal EPS-specific glycosylhydrolase activity ofpurified PssZ. FIG. 17A shows SDS-PAGE of purified recombinant proteins.S, protein standards; lane 1, PssZ E72Q; lane 2, PssZ. Molecular weightsof protein standards are given in kDa. FIG. 17B shows alignment of PssZproteins (residues 48-159) with the HMM alignment for GH8 familyproteins. The active site Glu72 conserved in GH8 proteins is shown inred. This residue was substituted with glutamine in the PssZ E72Qmutant. Other conserved residues are indicated in blue. #HMM, consensusof the Hidden Markov Model (HMM) (SEQ ID NO: 62); #MATCH, the matchbetween the query sequence and the HMM; #PP, posterior probability (adegree of certainty for each aligned residue, i.e., asterisk indicatesthe highest certainty). #Lin, L. innocua Lin2027 (SEQ ID NO: 63); #Lmo,L. monocytogenes PssZ (Lmo 1913) (SEQ ID NO: 64). Note: the alignment isdivided into two parts of the ease of illustration. FIG. 17C shows acell aggregation assay with the ΔpdeB/C/D strain in the presence of PssZand PssZ E72Q. Cells were grown in HTM/G at 30° C. for 24 h in thepresence of added recombinant proteins. Protein concentrations: panel 1,0.13 μg mL⁻¹; panel 2, 1.3 μg mL⁻¹. FIG. 17D shows dispersal ofpreformed aggregates with PssZ. Proteins were added at 32 μg mL⁻¹ (finalconcentration) to the washed aggregates of strain ΔpdeB/C/D andincubated with gentle shaking in HTM salts (no glucose) for 6 h at 30°C.

FIGS. 18A-18B: Diguanylate cyclases (DGCs), DgcA and DgcB, controlManNAc-Gal EPS synthesis in L. monocytogenes. FIG. 18A shows a Congo redbinding assay with ΔpdeB/C/D strains with in-frame deletions in the DGCgenes. FIG. 18B shows a cell aggregation assay with ΔpdeB/C/D strainswith in-frame deletions in the DGC genes. 1, ΔpdeB/C/D; 2, ΔpdeB/C/DΔdgcA; 3, ΔpdeB/C/D ΔdgcB; 4, ΔpdeB/C/D ΔdgcC; 5, ΔpdeB/C/D ΔdgcA/B.FIG. 18C shows aggregation of ΔpdeB/C/D strains with in-frame deletionsin the DGC genes assessed by drop in optical density. The drop in theoptical density correlates with the degree of cell aggregation. Data arederived from two independent biological repeats each with threemeasurements.

FIG. 19: Model for listerial c-di-GMP-regulated ManNAc-Gal EPSbiosynthesis machinery. The signaling molecule c-di-GMP (red diamond) issynthesized from GTP by DGCs, DgcA, and DgcB. pGpG (p, phosphate; G,guanine) is the breakdown product of c-di-GMP hydrolysis byphosphodiesterase PdeC. Proteins involved in ManNAc-Gap EPS biosynthesisare depicted according to their predicted localizations. Barrels,protein transmembrane domains. Arrows indicate the reactions catalyzedby DgcA/B and PdeC proteins. Green squares, N-acetylmannosamine(ManNAc); yellow circles, galactose (Gal).

DETAILED DESCRIPTION OF THE INVENTION

Throughout this disclosure, various publications, patents, and publishedpatent specifications may be referenced. The disclosures of thesepublications, patents, and published patent specifications are herebyincorporated by reference into the present disclosure to more fullydescribe materials and methods which may be used in conjunction withaspects of the described invention.

Listeria monocytogenes produces an N-acetylmannosamine (ManNAc)-basedexopolysaccharide (EPS), also designated as the Pss EPS, that protectsit against desiccation and commonly used disinfectants, including bleachand hydrogen peroxide. For example, exopolysaccharide-aggregatedlisterial cells show>10⁶-fold higher survival rates when treated withbleach, compared to non-aggregated bacteria. In accordance with thepresent disclosure, the L. monocytogenes enzyme referred to herein asPssZ efficiently degrades listerial exopolysaccharide. The sequence ofthe gene and protein, as well as methods of recombinant PssZpurification from E. coli, and methods of using PssZ for the uses suchas listerial aggregate disintegration and prevention of aggregation, arenow described herein. The structure of the listerial ManNAc-basedexopolysaccharide is unique. PssZ is the first enzyme that can degradelisterial exopolysaccharide.

The addition of recombinant PssZ to L. monocytogenes-containing mediaprevents formation of exopolysaccharide-rich aggregates. Therefore, PssZcan be used, separately or in combination with disinfectants, todisintegrate bacterial exopolysaccharide-rich aggregates and increasethe efficiency of disinfection. PssZ may also be used as a food additiveto prevent formation of exopolysaccharide-rich aggregates in the foodsprone to contamination by L. monocytogenes or other pathogenic bacteriaproducing ManNAc-based exopolysaccharide.

L. monocytogenes undergoes a transformation from a soil-borne bacterialsaprophyte to a life-threatening intracellular pathogen. L.monocytogenes causes the food-borne disease listeriosis, which is arelatively rare and yet highly fatal disease with a mortality rate of20-25%. It follows Salmonella as the second leading cause of death dueto food-borne bacterial outbreaks in the USA, where the annual healthcosts associated with listeriosis are estimated to be ˜$8.8 billion peryear. In recent years, the listeriosis incidence rate has beenincreasing in the USA and Europe. The elderly, immunocompromisedindividuals, newborns, and pregnant women are at high risk forlife-threatening listeriosis with variable clinical manifestations suchas meningitis, sepsis, bacteremia, miscarriages and stillbirth. Inhealthy individuals, L. monocytogenes causes flu-like symptoms andgastroenteritis.

Listeriosis can occur after consumption of food products contaminatedwith relatively high numbers (approximately 10⁶) of L. monocytogenescells. The food vehicles reported in listeriosis outbreaks have beendeli meats, frankfurters, cheese made from unpasteurized milk, salads,sprouts, and cantaloupes. Postprocess food contamination is commonbecause L. monocytogenes persists in food processing plants,contaminates final products, and eventually reaches high numbers infoods. Indeed, L. monocytogenes can survive and multiply in harshconditions owing to its ability to grow at cold temperatures, tolerateacidic and osmotic stresses and disinfectants, and form long-persistingbiofilms. Some of these features have been attributed to specifictranscriptional regulators, alternative sigma factors, two-componentsystems, transport proteins, and stress tolerance systems.

L. monocytogenes can produce a ManNAc)-based EPS. Cells embedded in EPSaggregates are much more tolerant to various disinfectants and tolong-term desiccation. Therefore, listerial EPS is an important factorfor listerial persistence in the environment and for food safety. TheEPS biosynthesis is linked to the pssA-E operon (lmo0527-lmo0531) in L.monocytogenes EGD-e. Two genes from this operon, pssC and pssE, havebeen found to be critical for EPS biosynthesis. pssC encodes a putativeglycosyltransferase, and pssE encodes an I-site type receptor for thebacterial second messenger, c-di-GMP, which is required for activatingEPS biosynthesis via the c-di-GMP-binding protein, PssE. C-di-GMPregulation of EPS biosynthetic complexes has been observed inproteobacteria. For instance, the glycosyltransferase BcsA, responsiblefor cellulose synthesis in many proteobacteria, binds c-di-GMP via aPilZ domain. Alginate biosynthesis in Pseudomonas aeruginosa is alsoregulated by the PilZ domain protein Alg44. However, the regulation ofthe P. aeruginosa Pel EPS synthase is also activated via an I-site typec-di-GMP receptor.

As described in the Examples herein, the evolutionary relationshipsamong the EPS biosynthesis proteins were assessed by performingphylogenetic analysis, which revealed that the listerial EPSbiosynthesis machinery has evolved within monoderms and that it is notclosely related to PNAG or cellulose biosynthesis proteins. The Examplesshow that listerial EPS is cell bound and that its chemical compositionis unique. Monosaccharide composition, linkage and NMR analyses indicatethat the trisaccharide repeating unit of the EPS polymer is{4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, where ManpNAc isN-acetylmannosamine and Galp is galactose. Using genetic analysis, itwas determined that all genes in the pssA-E operon, as well as the pssZ(lmo1913) gene located elsewhere, are required for EPS production andthat PssZ functions as an EPS specific glycosylhydrolase. Furthermore,two diguanylate cyclases (DGCs) primarily responsible forc-di-GMP-dependent activation of listerial EPS synthesis were uncovered.

The PssZ protein, also referred to as Lmo1913, has the sequence:

[SEQ ID NO: 1] MKRFILILILLIFIGAGFFIFLRPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHFFDYINKEITLKK.In accordance with the present disclosure, the PssZ protein, and alsotruncated fragments, mutants, and variants thereof, is useful forhydrolyzing a listerial exopolysaccharide, disintegrating bacterialaggregates, and disinfecting various articles contaminated withlisterial bacteria. In particular embodiments, the PssZ protein is usedwithout the transmembrane domain of the protein, thus having thesequence:

[SEQ ID NO: 2] RPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHF FDYINKEITLKK.

Amino acid sequence variants of the PssZ protein are encompassed withinthe present disclosure. Modifications to the PssZ protein can beintroduced by mutagenesis or protein synthesis. Such modificationsinclude, for example, deletions from, insertions into, and/orsubstitutions within the amino acid sequence of PssZ. Any combination ofdeletion, insertion, and substitution can be made to arrive at the finalamino acid construct of the variant protein, provided that the finalconstruct possesses the desired solubility and biological activity, suchas the enzymatic activity of PssZ. Accordingly, provided herein arevariants of the PssZ protein. In some embodiments, the variants have atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%sequence identitity to the amino acid sequence of PssZ. Reference to a“% sequence identity” with respect to a reference polypeptide is definedas the percentage of amino acid residues in a candidate sequence thatare identical with the amino acid residues in the reference polypeptide,after aligning the sequences and introducing gaps, if necessary, toachieve the maximum percent sequence identitity, and not considering anyconservative substitutions as part of the sequence identity.

One non-limiting example of a suitable PssZ fragment has the sequence:

[SEQ ID NO: 2] RPESKKTVSAPKETTPTSTSVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFIAEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTINADPFFTEVFQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHF FDYINKEITLKK.One non-limiting example of a suitable PssZ mutant, referred to hereinas a E72Q mutant, has the sequence of PssZ with a Glu72 site substitutedwith glutamine.

EXAMPLES Example I

This Example describes the characterization of key components and majortargets of the c-di-GMP signaling pathways in the foodborne pathogenListeria monocytogenes, the identification of a c-di-GMP-inducibleexopolysaccharide responsible for motility inhibition, cell aggregation,and enhanced tolerance to disinfectants and desiccation, and theelucidation of the role of c-di-GMP signaling in listerial virulence.

Genome-wide genetic and biochemical analyses of c-di-GMP signalingpathways revealed that L. monocytogenes has three GGDEF domain proteins(“GGDEF” disclosed as SEQ ID NO: 3), DgcA (Lmo1911), DgcB (Lmo1912), andDgcC (Lmo2174), that possess diguanylate cyclase activity, and three EALdomain proteins, PdeB (Lmo0131), PdeC (Lmo1914), and PdeD (Lmo0111),that possess c-di-GMP phosphodiesterase activity. Deletion of allphosphodiesterase genes (ΔpdeB/C/D) or expression of a heterologousdiguanylate cyclase stimulated production of a previously unknownexopolysaccharide. The synthesis of this exopolysaccharide wasattributed to the pssA-E (lmo0527-0531) gene cluster. The last gene ofthe cluster encodes the fourth listerial GGDEF domain protein (“GGDEF”disclosed as SEQ ID NO: 3), PssE, that functions as an I-site c-di-GMPreceptor essential for exopolysaccharide synthesis. Thec-di-GMP-inducible exopolysaccharide causes cell aggregation in minimalmedium and impairs bacterial migration in semi-solid agar, however, itdoes not promote biofilm formation on abiotic surfaces. Theexopolysaccharide also greatly enhances bacterial tolerance to commonlyused disinfectants as well as desiccation, which may contribute tosurvival of L. monocytogenes on contaminated food products and infood-processing facilities. The exopolysaccharide and another, as yetunknown c-di-GMP-dependent target, drastically decrease listerialinvasiveness in enterocytes in vitro, and lower pathogen load in theliver and gallbladder of mice infected via an oral route, whichindicates that elevated c-di-GMP levels play an overall negative role inlisterial virulence.

Cyclic dimeric GMP (c-di-GMP) is one of the most common bacterial secondmessengers. The understanding of c-di-GMP-mediated signal transductionpathways has rapidly expanded. However, this expansion has beendominated by studies of Proteobacteria, and to a lesser extentActinobacteria and Spirochetes, while studies of c-di-GMP signaling inFirmicutes have been lacking. In the Proteobacteria, elevated levels ofintracellular c-di-GMP are associated with inhibition of motility andincreased synthesis of biofilm components, e.g. exopolysaccharides(EPS), pili, and/or surface adhesins. In pathogens that propagateextracellularly, elevated c-di-GMP levels have been found generallydetrimental for acute infections, although individual components ofc-di-GMP signaling networks may play different roles during variousstages of infection. In contrast, during chronic infections,c-di-GMP-induced biofilms greatly increase pathogen survival in vivo. Inintracellular proteobacterial pathogens, c-di-GMP signaling pathways arerequired for full-scale virulence in those species that formbiofilm-like intracellular structures, but appear to be detrimental, atleast in some species, that do not form such structures.

In this Example, the foodborne pathogen Listeria monocytogenes was usedto gain insight into c-di-GMP-based regulation in Firmicutes in general.L. monocytogenes is widespread in the environment. It has been isolatedfrom soil, silage, groundwater, sewage, and vegetation, and activelygrows at a broad range of temperatures (from 0 to 44° C.), oxygenlevels, pH (from 4.4 to 9.6), and salt concentrations (up to 10% w/vNaCl), and is capable of utilizing a variety of carbohydrates as well asother organic molecules as carbon sources. Listeriosis is a relativelyinfrequent disease but it has the highest mortality rate, ˜20%, amongfoodborne diseases in the developed world. The complications oflisteriosis, common in immunocompromised patients, include encephalitis,meningitis, and stillbirths or infection of the central nervous systemin newborns.

Common sources of listerial contamination include unpasteurized milk andmilk products, raw meat, and packaged cooked meat products. In plantsprocessing meat and milk products listerial biofilms can persist foryears and even decades and cause repetitive contamination of processedfoods. In recent years, listeriosis caused by contaminated fresh producehas become a significant concern. According to The Centers for DiseaseControl and Prevention, the 2011 outbreak caused byListeria-contaminated cantaloupes resulted in 33 deaths and was thelargest foodborne disease outbreak in US history in almost 90 years. Theunderstanding of how listeria attach and grow on the surfaces of produceis surprisingly poor, and so is the knowledge of the mechanisms ensuringlong-term listerial survival. EPS is one of the common components thatfacilitate bacterial attachment to plant surfaces and increases theirtolerance to desiccation and disinfection, both of which are criticalparameters for food safety. However, the ability of L. monocytogenes tosynthesize EPS has remained controversial.

In Proteobacteria, EPS synthesis is commonly induced via c-di-GMPsignaling pathways, yet studies of such pathways in Firmicutes arelacking. It is peculiar that distribution of c-di-GMP signaling pathwaysin Firmicutes is very uneven. Several major genera of pathogenicfirmicutes, Staphylococci, Streptococci and Enterococci, lack thesealtogether. However, staphylococci retain remnants of c-di-GMP signalingenzymes, which are involved in biofilm regulation but are no longerassociated with c-di-GMP. On the other extreme of the spectrum arecertain clostridial species, e.g. Clostridium difficile, that havenumerous enzymes involved in c-di-GMP synthesis and hydrolysis. It hasbeen observed that elevated levels of c-di-GMP inhibited motility andinduced cell aggregation in C. difficile. The c-di-GMP-dependentriboswitches from C. difficile expressed in a heterologous have beenshown to affect gene expression in a c-di-GMP-dependent manner. Oneriboswitch is located upstream of the C. difficile flagellarbiosynthesis operon; the other one is part of the riboswitch-ribozymesystem predicted to control adhesin gene expression. Enzymes involved inc-di-GMP synthesis and degradation in Bacillus subtilis have beenidentified, and the role of c-di-GMP in regulating motility and biofilmformation in this species has been characterized.

In this Example, a genome-wide view of c-di-GMP signaling in L.monocytogenes is presented. Bioinformatics analysis was used to identifygenes involved in c-di-GMP synthesis, degradation and signaltransduction. Subsequently, genetic and biochemical approaches wereapplied to characterize functions of these genes in EPS synthesis,motility inhibition, tolerance to disinfection and desiccation,invasiveness in mammalian cells, and virulence in a mouse model oflisteriosis.

Results

Bioinformatic Analysis of the c-di-GMP Signaling System in Listeria

C-di-GMP is synthesized by diguanylate cyclases (DGCs), which containGGDEF domains (“GGDEF” disclosed as SEQ ID NO: 3), and degraded byc-di-GMP-specific phosphodiesterases (PDEs), which contain either EAL orHD-GYP catalytic domains. The currently sequenced strains of L.monocytogenes, and the majority of related listerial species, encodefour GGDEF domain proteins (“GGDEF” disclosed as SEQ ID NO: 3), threeEAL domain proteins, and no HD-GYP domain proteins (FIG. 1).

The sequence analysis indicated that three of the four GGDEF proteins(“GGDEF” disclosed as SEQ ID NO: 3) from L. monocytogenes EGD-e, Lmo1911(DgcA), Lmo1912 (DgcB), and Lmo2174 (DgcC), contain conserved residuesassociated with DGC activity, and therefore they possess DGC activities.The three indicated DGCs have similar domain architectures with a GGDEFdomain (“GGDEF” disclosed as SEQ ID NO: 3) preceded by either six oreight transmembrane helices (FIG. 1). This domain architecture indicatesthat c-di-GMP synthesis is regulated by external signals or signalsderived from the cell wall or cytoplasmic membrane. The three proteinsshare approximately 30% identity to each other over their entirelengths, and may have resulted from ancient gene duplications. The EALdomain proteins in strain EGD-e, Lmo0131 (PdeB), Lmo1914 (PdeC), andLmo0111 (PdeD), have conserved residues required for c-di-GMP bindingand hydrolysis, and therefore are believed to possess PDE activities(FIG. 1). These putative PDEs contain only single EAL domains,indicating their cytoplasmic localization.

The dgcA and dgcB genes are codirectional and separated from each otherby 20 bp, which indicates that they form an operon. The pdeC geneappears to belong to the same dgcA-dgcB-lmo1913-pdeC (lmo1911-1914)operon. Tiling microarray expression data support an operonal structureof this gene cluster. The intervening gene, lmo1913, encodes a proteinof as-of-yet unknown function. Based on structural predictions, Lmo1913belongs to the six-hairpin glycosidase superfamily (FIG. 1). Therefore,DgcA, DgcB, and PdeC may represent a signaling module involved inc-di-GMP synthesis and degradation, and this module may be involved incontrolling synthesis of an unknown EPS.

The GGDEF domain (“GGDEF” disclosed as SEQ ID NO: 3) of the fourth GGDEFprotein (“GGDEF” disclosed as SEQ ID NO: 3), Lmo0531, is degenerate. Thesignature GG(D/E)EF motif (SEQ ID NO: 5) in Lmo531 is ²⁰⁸DKDDA (SEQ IDNO: 6), which should make this protein incapable of c-di-GMP synthesis(FIG. 1). Five amino acids upstream of the signature motif is an RxxDmotif that represents a part of a c-di-GMP-binding sequence known as anI-site. Therefore, without wishing to be bound by theory, it is believedthat Lmo0531 acts as a c-di-GMP receptor/effector protein similar to theI-site containing degenerate GGDEF domain proteins (“GGDEF” disclosed asSEQ ID NO: 3). It is peculiar that Lmo0531 is the only c-di-GMP receptorthat can be predicted based on genome sequence analysis.

To test functions of the L. monocytogenes DGC and PDE proteins and asingle identifiable c-di-GMP receptor, these genes were cloned andexpressed in E. coli indicator strains that respond to changes inintracellular c-di-GMP concentrations in a predictable fashion. Wherenecessary, proteins were purified to test their activities in vitro.

L. Monocytogenes PdeB-D Proteins Possess c-di-GMP PDE Activities

L. monocytogenes pdeB, pdeC, and pdeD were expressed in E. coli MG1655ΔyhjH. This mutant lacks a major c-di-GMP PDE, YhjH, and as a result, isimpaired in motility in semi-solid agar. It was found that expression ofany one of the pde genes was sufficient to partially restore swim zonesof MG1655 ΔyhjH in semi-solid agar (FIG. 2A). These results areconsistent with all three proteins, PdeB, PdeC, and PdeD, functioning asc-di-GMP PDEs. However, overexpressed but enzymatically inactive EALdomain proteins that retain the ability to bind (but not to hydrolyze)c-di-GMP also can lower intracellular c-di-GMP concentration, thusmimicking the phenotypes of overexpressed PDEs.

To resolve the ambiguity regarding the enzymatic activity of the PdeB-Dproteins, each protein was purified and tested for its ability tohydrolyze c-di-GMP in vitro. The PdeB and PdeD proteins wereoverexpressed and purified as N-terminal His₆-tagged fusions (“His₆”disclosed as SEQ ID NO: 4). Since the His₆-tagged PdeC fusion (“His₆”disclosed as SEQ ID NO: 4) proved to be insoluble, PdeC was purified asa fusion to maltose-binding protein (MBP) (FIG. 2B). The ability ofpurified PdeB, PdeC, or PdeD to hydrolyze c-di-GMP was assessed bymeasuring the substrate and products of reactions over time using HPLC.FIG. 2C shows that all three recombinant proteins possess c-di-GMP PDEactivities in vitro.

L. Monocytogenes DgcA-C Proteins Possess DGC Activities

The functionality of putative L. monocytogenes DGC proteins was assessedby monitoring swim zone sizes in semi-solid agar. The three dgc geneswere cloned into the pBAD/Myc-His vector under the control of anarabinose-inducible promoter. Each of the three dgc genes decreased, tovarious degrees, the sizes of the swim zones of strain MG1655, which ishighly motile in the absence of heterologous DGCs (FIG. 3A).

To exclude the possibility of nonspecific motility inhibition (e.g., dueto protein toxicity), a second c-di-GMP-dependent phenotype that isindependent of motility inhibition was assessed. In E. coli BL21 (DE3),c-di-GMP induces synthesis of curli fimbriae that can be detected bystaining with Congo red dye. As shown in FIG. 3B, BL21 (DE3) strainsexpressing each of the three Dgc proteins individually exhibited moreintensely colored colonies on Congo red agar compared to the negativecontrol expressing an empty vector. Together, these results indicatethat the DgcA-C proteins possess DGC activity.

L. Monocytogenes Phenotypes Associated with Perturbed Intracellularc-di-GMP Levels

Having established that L. monocytogenes EGD-e possesses functionalcomponents for c-di-GMP-mediated signaling, phenotypes associated withelevated and decreased intracellular c-di-GMP levels were examined. Toperturb c-di-GMP levels, two c-di-GMP metabolizing enzymes, DGC (Slr1143from Synechocystis sp.) and PDE (YhjH from E. coli), were expressed inthe EGD-e strain and assessed for their role in swimming motility andEPS production. The use of heterologous proteins allowed the effects ofchanging intracellular c-di-GMP levels to be assessed without undesiredchanges in protein-protein interactions that may have occurred iflisterial DGC and PDE enzymes were overexpressed.

L. monocytogenes uses flagella for motility. Expression of Slr1143blocked swimming of strain EGD-e in semi-solid agar, whereas expressionof YhjH had no effect (FIG. 4A, top). Expression of Slr1143 alsoresulted in more pigmented L. monocytogenes colonies on Congo red agar,whereas expression of YhjH had no observable phenotype (FIG. 4B, sectors10 versus 1 and 9). Later in this Example, it is shown that YhjH isexpressed and functional as a PDE in L. monocytogenes. Therefore, thelack of a phenotype associated with YhjH overexpression is interpretedas an indication that intracellular c-di-GMP levels in strain EGD-e arealready low, and that c-di-GMP does not play a significant role underthe conditions used in these assays. Since L. monocytogenes is not knownto synthesize pili, and the genome of strain EGD-e has no candidate piligenes, Congo red staining was indicative of EPS production. An EPS hasbeen suspected in some naturally occurring L. monocytogenes isolates.Further, Congo red staining rings within L. monocytogenes coloniesexposed to dark-light cycles has been observed. However, the nature ofthe Congo red-binding extracellular polymer was not investigated.

Construction and Characterization of the L. Monocytogenes dgc and pdeMutants

Having identified two phenotypes associated with elevated c-di-GMPlevels, the L. monocytogenes pdeB-D genes were inactivated, individuallyand in combination. Based on the inhibition of swim zones in semi-solidagar by the heterologous DGC, Slr1143, it was believed that pdeB-Dmutations would result in smaller swim zones. However, inactivation ofindividual pde genes did not significantly affect swim zone sizes (FIG.4C). Inactivation of pairs of pde genes produced relatively minordecreases in swim zones sizes, while simultaneous deletion of all threepde genes, ΔpdeB/C/D, produced a mutant severely impaired in swimming insemi-solid agar (FIG. 4C). This phenotype is similar to the phenotype ofthe wild type EGD-e expressing the heterologous DGC, Slr1143 (FIG. 4A,top). These results indicate that the PDEs have at least partiallyoverlapping functions in degrading intracellular c-di-GMP.

Expression of Slr1143 in the triple ΔpdeB/C/D mutant did not affect thealready inhibited motility any further (FIG. 4A, bottom). However,expression of YhjH in this mutant fully restored the swim zone to thesize of the wild-type strain, thus showing that YhjH is expressed andfunctional in L. monocytogenes (FIG. 4A, bottom), and that motilityinhibition in semi-solid agar was due to elevated c-di-GMP levels in thetriple ΔpdeB/C/D mutant.

The effects of L. monocytogenes pde mutations on Congo red binding weretested. The triple ΔpdeB/C/D mutant showed significant accumulation ofCongo red (FIG. 4B, sector 2 versus 1), similar to the wild type strainexpressing Slr1143 (FIG. 4B, sector 10). Expression of YhjH, but notSlr1143, in the triple ΔpdeB/C/D mutant, inhibited Congo redaccumulation (FIG. 4B, sector 6 versus 5 or 7). Individual pde mutantsdid not affect Congo red staining, while among double mutants, thepdeB/C mutant showed some staining.

In addition to Congo red binding, the colonies of the ΔpdeB/C/D mutantwere found to have rough edges, compared to smooth-edged colonies of thewild type strain (FIG. 4D). The observed changes in colony morphology inthe ΔpdeB/C/D mutant were not as pronounced as the wrinkled or roughcolony morphologies reported in the proteobacterial speciesoverexpressing EPS, however, when combined with enhanced Congo redbinding, these changes are indicative of EPS production.

Inactivation of the dgc genes, individually or in combination, resultedin no observable phenotypes, just like the expression of YhjH in thewild type strain produced no phenotype. It is therefore concluded thatc-di-GMP plays little, if any, role in strain EGD-e grown under theselaboratory conditions.

Bioinformatics-Based Identification of the Putative EPS BiosynthesispssA-E Operon in L. Monocytogenes

The L. monocytogenes genome was searched for EPS biosynthesis genes thatcould be responsible for c-di-GMP-induced Congo red binding. Thelmo0527-0531 operon, designated here pssA-E (polysaccharide synthesis)(FIG. 1), emerged as the prime candidate for this role based on thefollowing reasoning. The last gene of the operon, pssE (lmo0531),encodes a degenerate GGDEF domain protein (“GGDEF” disclosed as SEQ IDNO: 3), believed to function as a c-di-GMP receptor (FIG. 1). If thisbelief is correct, PssE may be involved in a c-di-GMP-dependentactivation of EPS synthesis, similar to activation of cellulose,alginate, and Pel EPS synthesis in Proteobacteria. An additional reasonto implicate the pssA-E cluster in EPS biosynthesis was based on thepresence of the putative glycosidase gene, lmo1913, in thedgcA-dgcB-lmo1913-pdeC operon that encodes enzymes for synthesis andhydrolysis of c-di-GMP (FIG. 1). Glycosidases counterbalanceglycosyltransferases and are integral components of EPS synthesis anddegradation apparati.

Without wishing to be bound by theory, it is believed the pssA-E operonencodes enzymes associated with biosynthesis ofpoly-β-1,6-N-acetyl-D-glucosamine (PNAG) or poly-β-1,4-D-glucopyranose(cellulose), either of which is capable of binding Congo red, or yetanother EPS. The key player in this operon is PssC (Lmo0529), which isbelieved to function as type 2 glycosyltransferase responsible for thepolymerization reaction. PssC shows the highest (˜30%) identity (over an˜300 amino acid region) to the N-acetylglycosyltransferases involved inPNAG synthesis from S. aureus (IcaA) and Yersinia pestis (HmsR).However, no other genes found in the staphylococcal ica or yersinial hmsgene clusters are present in the pssA-E operon. Instead, the genedownstream of pssC, pssD (1m0530), encodes an ortholog of the BcsBsubunit of bacterial cellulose synthases. The BcsB proteins have thusfar been associated exclusively with cellulose synthases, yet they areinvolved in the membrane passage of the polysaccharide polymer not itssynthesis, therefore BcsB is believed to be able to accommodate polymersof different composition than cellulose. It is noteworthy that theglycosyltransferases catalyzing cellulose synthesis also belong to type2 glycosyltransferases, like the PNAG synthases. Further, PssCshares˜25% identity with the type 2 glycosyltransferase BcsA of thecellulose synthase complex of Rhodobacter sphaeroides. The almost equalsimilarity of the listerial glycosyl transferase to PNAG- and cellulosesynthases makes predictions of the composition of the listerial EPSunreliable.

The pssA-E Gene Cluster is Responsible for Listerial EPS Synthesis

To test the involvement of the pssA-E gene cluster in EPS biosynthesis,the believed glycosyltransferase gene, pssC, was deleted in theΔpdeB/C/D background. It was found that the constructed ΔpdeB/C/D ΔpssCmutant no longer bound Congo red (FIG. 4B, sector 4). This resultindicates that the pssA-E operon is responsible for c-di-GMP-induced EPSbiosynthesis. To verify it further, whether inactivation of pssE in theΔpdeB/C/D background will also impair EPS synthesis was tested. Indeed,the constructed ΔpdeB/C/D ΔpssE mutant did not bind Congo red either(FIG. 4B, sector 3). It is concluded that PssE, a putative c-di-GMPreceptor, plays a critical role in EPS synthesis. Complementation of theΔpdeB/C/D ΔpssC and ΔpdeB/C/D ΔpssE mutants with individually clonedpssC and pssE, respectively, restored Congo red binding, verifying thatthe ΔpssC and ΔpssE mutations were responsible for the mutantphenotypes. The ΔpssC and ΔpssE mutations in the ΔpdeB/C/D mutantbackground reversed the rough colony phenotype back to a smoothappearance (FIG. 4D).

Biochemical Evidence that the PssE Protein is a c-di-GMP Receptor

To test the prediction that the PssE protein acts as a c-di-GMPreceptor, its GGDEF domain (“GGDEF” disclosed as SEQ ID NO: 3)containing the I-site as an MBP fusion (MBP-GGDEF_(pssE)) (“GGDEF”disclosed as SEQ ID NO: 3) was overexpressed, and this protein waspurified (FIG. 5A) and analyzed for its ability to bind c-di-GMP invitro using equilibrium dialysis. MBP-GGDEF_(pssE) (“GGDEF” disclosed asSEQ ID NO: 3) was found to bind c-di-GMP with an apparent K_(d) of0.79±0.17 μM (FIG. 5B). This value falls within the range ofphysiologically relevant intracellular c-di-GMP concentrations measuredin other bacteria that are believed to be in the submicromolar to lowmicromolar range. The binding capacity of the MBP-GGDEF_(pssE) protein(“GGDEF” disclosed as SEQ ID NO: 3), B_(max), was calculated to be2.03±0.12 μM c-di-GMP (μM protein)⁻¹ indicating that each PssE moleculecan bind two c-di-GMP molecules at saturation. This result is consistentwith the observation of an intercalated c-di-GMP dimer bound to theI-sites of crystallized GGDEF domain proteins (“GGDEF” disclosed as SEQID NO: 3). Therefore, PssE is a bona fide c-di-GMP receptor that ispredicted to transfer the c-di-GMP signal to activate synthesis of thelisterial Pss EPS.

C-di-GMP-Induced Listerial EPS Promotes Cell Aggregation but PlaysLimited Role in Biofilm Formation on Abiotic Surfaces

PNAG and cellulose increase biofilm formation by the proteobacterialspecies on abiotic surfaces. To test the effect of c-di-GMP-induced EPSin L. monocytogenes, a conventional Crystal violet dye-binding assaythat measures the biomass of cells attached to the wells of microtiterplates following removal of liquid cultures was performed. Surprisingly,an increase in biofilm levels in the ΔpdeB/C/D mutant, compared to thewild type, was not observed when these strains were grown in LB medium(where biofilm formation of strain EGD-e is low). Only a marginalincrease in surface-attached biofilm levels in LB supplemented withglycerol (where biofilms are greatly stimulated) was observed (FIG. 6A).Interestingly, this increase in biofilm levels was observed in allΔpdeB/C/D strains grown in LB plus glycerol, whether or not theyproduced EPS (FIG. 6A). These results indicate that, instead of theanticipated stimulation of biofilms, listerial EPS actually inhibitsbiofilm formation, at least under certain conditions. These results alsoimplicate a c-di-GMP-activated non-EPS component in biofilm stimulation.Similar to the results on polystyrene surfaces, the ΔpdeB/C/D mutantproduced no more biofilm in LB medium on glass or metal (aluminum foilor steel coupons) surfaces than did the wild type.

It was noticed that incubation of the ΔpdeB/C/D mutant (but not the wildtype, ΔpdeB/C/D ΔpssC or ΔpdeB/C/D ΔpssE mutants) in liquid glucose-richminimal HTM medium resulted in cell clumping (FIG. 6B). This indicatesthat listerial EPS strengthens intercellular interactions but notbacterial interactions with abiotic surfaces. The pssC and pssE genedeletions in the ΔpdeB/C/D background completely abolished clumping,just like they decreased Congo red binding in BHI plates. This resultconfirms that listerial EPS is responsible for clumping.

C-di-GMP-Dependent EPS Impairs L. Monocytogenes Motility in Semi-SolidAgar

Since the EPS producing ΔpdeB/C/D mutant was impaired in swimming insemi-solid agar (FIG. 4C), the effect of EPS on motility was evaluated.Surprisingly, inactivation of EPS synthesis by the pssC or pssEmutations, restored swimming of the ΔpdeB/C/D mutant in semi-solid agarto the wild-type levels (FIG. 4E). Therefore, swimming in semi-solidagar was impaired exclusively due to listerial EPS.

To gain additional insight into this issue, the motility of the wildtype, the ΔpdeB/C/D mutant, and the ΔpdeB/C/D ΔpssC mutant were analyzedin liquid medium where clumping is minimal and not detectable by thenaked eye. Phase contrast microscopic observations revealed that singlecells of the ΔpdeB/C/D and ΔpdeB/C/D ΔpssC mutants were as motile as thewild-type cells. These results favor the scenario whereby EPSaccumulated on cell surfaces results in cell aggregation, which inhibitsspreading of the cells in semi-solid agar.

C-di-GMP-Induced EPS Significantly Enhances L. Monocytogenes Toleranceto Disinfectants and Desiccation

EPS is known to protect bacteria from environmental insults. Here, therole of L. monocytogenes EPS in providing tolerance to disinfection anddesiccation was evaluated. The wild-type strain EGD-e as well as itsΔpdeB/C/D mutant synthesizing EPS and grown under clump-formingconditions were subjected to selected disinfectants commonly used in thefood-processing industry and produce storage facilities: sodiumhypochlorite (bleach), benzalkonium chloride (a quaternary ammoniumcompound), and hydrogen peroxide. To distinguish between thecontribution of EPS versus EPS-independent c-di-GMP-responsive agents,included in the tests were the ΔpdeB/C/D ΔpssC mutant characterized byelevated intracellular c-di-GMP levels but defective in EPS production.

The sodium hypochlorite treatment applied here was highly effective inkilling the wild-type strain, but not the EPS producing ΔpdeB/C/Dmutant, whose survival was approximately >10⁶-fold higher than thesurvival of the wild type (FIG. 6C). Tolerance of the ΔpdeB/C/D mutantto hydrogen peroxide and benzalkonium chloride treatments was alsohighly, approximately 10²-fold, higher, compared to the wild type or theEPS-deficient ΔpdeB/C/D ΔpssC mutant (FIG. 6C). These observationsindicate that the c-di-GMP-induced EPS is a critical factor responsiblefor increased tolerance to these agents.

EPS also enhanced survival of L. monocytogenes to long-term desiccation.In this Example, the liquid-grown cultures were centrifuged, and thepellets were kept in a desiccator for 7 or 21 days. It was found thatthe desiccation survival rates of the EPS producing ΔpdeB/C/D strainwere significantly higher, compared to those of the wild type or theΔpdeB/C/D ΔpssC mutant (FIG. 6D). These results indicate that EPSprovides superior protection not only against various commonly useddisinfectants in food processing plants but also to desiccation, whichmay enhance listerial survival during food transportation and storage.

Elevated c-di-GMP Levels Inhibit L. Monocytogenes Invasion intoMammalian Cells

As a foodborne pathogen, L. monocytogenes is expected to use gutepithelial cells for primary invasion. The consequences of elevatedc-di-GMP levels on bacterial invasion into HT-29 human colonadenocarcinoma cells were examined. As shown in FIG. 7A, the strainswith elevated c-di-GMP levels were significantly impaired in invasion,whether elevated c-di-GMP was caused by expression of the heterologousDGC, Slr1143, or by the ΔpdeB/C/D mutations. Consistent with theinhibitory role of c-di-GMP, invasion was increased, by approximately2-fold, in the L. monocytogenes strain expressing a c-di-GMP PDE, YhjH.

Next, what role the c-di-GMP-induced EPS may have played in invasioninhibition was tested. It was observed that the ΔpdeB/C/D ΔpssC andΔpdeB/C/D ΔpssE mutants showed approximately 2-2.5-fold greaterinvasiveness compared to the ΔpdeB/C/D mutant (FIG. 7B), but remainedapproximately 10-fold less invasive than the wild type strain. Theseresults indicate that while EPS moderately inhibits invasion, the majorreason for the defective invasion is a c-di-GMP-induced component(s)different from EPS. The nature of this component(s) and the mechanismsthrough which it inhibits listerial invasion remain to be investigated.

Elevated c-di-GMP Levels Reduce Systemic Spread of L. Monocytogenes inMice Infected Via an Oral Route

To assess the role of c-di-GMP signaling in vivo, we used a newlydeveloped mouse model of foodborne listeriosis. Groups of BALB/c/By/Jmice were fed either wild-type EGD-e or the ΔpdeB/C/D mutant, and thebacterial load in various tissues was assessed 60 h post infection.There was no significant difference in colonization of the ileum, colonor spleen at this time point (FIG. 8). However, the ΔpdeB/C/D triplemutant was significantly impaired in colonizing both the liver and thegallbladder. The decreased bacterial load in the liver appears to belinked to EPS, since the ΔpssC mutation in the ΔpdeB/C/D backgroundrestored the bacterial load to the wild-type level (FIG. 8). In fact, nosignificant differences in bacterial loads in the liver were observedwhen the same L. monocytogenes strains were injected intravenously,indicating that increased levels of c-di-GMP may alter the ability ofthe bacteria to disseminate from the gut.

Discussion

It was speculated that the L. monocytogenes EGD-e genome encodes threeGGDEF domain DGCs (“GGDEF” disclosed as SEQ ID NO: 3), one inactiveGGDEF domain protein (“GGDEF” disclosed as SEQ ID NO: 3) and three EALdomain PDEs. This belief was verified by a combination of genetic andbiochemical tests. Interestingly, all of the enzymes involved inc-di-GMP metabolism are highly conserved not only in the genomes of L.monocytogenes isolates but also in other Listeria species, e.g. L.innocua, L. ivanovii, L. seeligeri, and L. welshimeri. The highconservation of these proteins indicates that c-di-GMP signalingpathways play important roles in the evolutionary success of Listeria.Such conservation is striking in light of the flexibility in theorganization of c-di-GMP signaling pathways observed in otherFirmicutes. For example, in the genus Bacillus, the number of enzymesinvolved in c-di-GMP synthesis and hydrolysis varies from three toeleven; it varies from eight to forty in the genus Clostridium.

It was determined that c-di-GMP regulation affects at least two targetsin L. monocytogenes. One of these targets is a novel EPS (FIGS. 4B, 4D,6B). This finding resolves the long-standing controversy regarding theability of listeria to produce EPS. The second, and possibly additional,target of c-di-GMP regulation, whose identity remains unknown, appearsto be responsible for the drastic inhibition of listerial invasivenessin mammalian cells (FIG. 7), modest stimulation of biofilm formation onabiotic surfaces in LB supplemented with glycerol (FIG. 6A), and lowerpathogen accumulation in certain mouse organs following oral infection(FIG. 8).

In this Example, it is revealed that the c-di-GMP induced EPS issynthesized by the pssA-E operon. The composition of the listerial EPSis difficult to predict because, while some Pss proteins sharesimilarity to the components of cellulose synthases and PNAG synthases,other components are unique. Interestingly, in contrast to cellulose orPNAG, both of which promote biofilm formation on abiotic surfaces,listerial EPS either does not affect or inhibits biofilm formation onabiotic surfaces. Instead, it promotes cell aggregation, in minimalmedia (FIG. 6B). These observations indicate that the composition oflisterial EPS is different from cellulose or PNAG.

This Example identifies the mechanism through which c-di-GMP activatesEPS synthesis in L. monocytogenes. C-di-GMP binds to the I-site receptorPssE, whose gene is located in the pss operon, and whose function isessential for EPS biosynthesis. Bacterial cellulose synthases studiedthus far are activated via c-di-GMP-binding PilZ domains linked to theC-termini of BcsA subunits. The PNAG synthase of E. coli is activated byc-di-GMP binding to two subunits, PgaD and PgaC, one of which, PgaD, isproteolytically degraded in the absence of c-di-GMP. Perhaps the mostsimilar c-di-GMP-dependent mechanism to that operating in L.monocytogenes Pss synthase involves the Pseudomonas aeruginosa Pel EPSsynthase, which is activated via an I-site c-di-GMP receptor protein.

This Example shows that the L. monocytogenes Pss EPS is responsible formultiple phenotypes, i.e., cell aggregation, decreased motility insemi-solid media, moderate inhibition of invasiveness in mammaliancells, and drastically elevated tolerance to disinfectants anddesiccation. The latter effects of c-di-GMP-induced listerial EPS areparticularly noteworthy in light of the increasing frequency oflisterial outbreaks associated with produce. Without wishing to be boundby theory, it is believed that EPS contributes to enhanced survival oflisteria on produce surfaces during washing with disinfectants as wellas during transportation and storage of listeria-contaminated produce.It is also believed that listerial EPS contributes to bacterial survivalin food-processing facilities.

C-di-GMP-induced motility inhibition is common in Proteobacteria. One ofthe best-understood mechanisms of c-di-GMP-induced motility inhibitioninvolves YcgR, the PilZ-domain c-di-GMP backstop brake that operates inE. coli and related enteric bacteria. YcgR binds to the flagellar switchcomplex and, at elevated c-di-GMP concentrations, introduces arotational bias that decreases the frequency of flagella reversals andtherefore, the frequency of changes in swimming direction. The smooth,almost unidirectional, swimming results in bacteria being trapped inblind alleys of semi-solid agar. YcgR may also slow down rotatingflagella. A similar mechanism has been proposed for a PilZ domainprotein in B. subtilis, however important details have yet to beelucidated. A different mechanism of c-di-GMP-induced motilityinhibition was described in Caulobacter crescentus, where a PilZ domainreceptor affects the abundance of a flagellum assembly regulatorysubunit. B. subtilis has yet another mechanism of motility inhibitionthat involves a bifunctional protein EpsE that acts as a glycosyltransferase involved in EPS synthesis and as a molecular clutch thatdisengages the flagellum rotor from the membrane-localizedenergy-supplying stator. Whether an EpsE-like clutch operates in L.monocytogenes remains unknown, however it is clear that no clutch orbreak is induced by c-di-GMP because liquid-grown cells show no obviousmotility defects. The most striking observation is that inactivation ofPss synthesis is sufficient to restore motility in semi-solid agar.Therefore, listerial spreading in semi-solid agar appears to beinhibited due to cell aggregation and possibly flagella trapping in theEPS. A similar mechanism has been described in S. enterica, which athigh c-di-GMP levels, secretes cellulose.

Listerial EPS inhibits bacterial invasiveness in mammalian cells,however, only modestly, 2-2.5-fold, whereas an as yet unidentifiedc-di-GMP pathway is responsible for a much larger component ofinvasiveness inhibition. The composition of this new c-di-GMP signalingpathway remains unknown. In this regard, it is noteworthy that PssE isthe only c-di-GMP receptor that can be predicted based on the genomesequence analysis. Listeria lack other identifiable c-di-GMP receptorproteins or c-di-GMP-sensing riboswitches.

In addition to uncovering the role of c-di-GMP in vitro, its role invirulence was tested using a food borne mouse disease model that closelymimics human infection. It was found that elevated c-di-GMP levelsdecreased listerial infection in the liver, and that this defect couldbe restored by abolishing EPS biosynthesis. Thus, it is possible thatc-di-GMP induced EPS impairs the ability of L. monocytogenes to eitherefficiently disseminate from the intestine or to replicate and spreadfrom cell-to-cell in hepatocytes. While a significant defect in theability of the ΔpdeB/C/D mutant to invade HT-29 colon carcinoma cells invitro was observed, there was no difference in the ability of theΔpdeB/C/D mutant to colonize the murine intestines, compared to the wildtype strain. Thus, increased c-di-GMP levels may impair the directinvasion of intestinal epithelial cells mediated by InlA/E-cadherininteractions, but does not significantly impede the ability of L.monocytogenes to translocate across the gut mucosa barrier, presumablybecause the bacteria use alternate mechanisms of invasion. L.monocytogenes can transcytose across M cells, specialized epithelialcells that are found both overlying Peyer's patches and scatteredelsewhere throughout the epithelium. It is also possible thatspecialized subsets of dendritic cells in the intestinal lamina propriacan engulf L. monocytogenes by extending dendrites into the gut lumen, aprocess that has been demonstrated during oral S. enterica infection.

Another issue pertaining to this Example concerns the role of cyclicdinucleotides as bacterial biomarkers recognized by the innate immunesystem and in the stimulation of the host intracytoplasmic surveillanceresponse. The listerial second messenger c-di-AMP, which is structurallyrelated to c-di-GMP, has been shown to be secreted into the cytosol ofinfected mammalian cells where it triggers interferon (IFN) productionvia the STING-signaling cascade. A robust IFNβ response promotes thegrowth of L. monocytogenes administered intravenously. This Exampleshows that the ΔpdeB/C/D mutant, which likely has the highest c-di-GMPproduction achievable during L. monocytogenes intracellular growth, wasoverall less infective following oral infection. This indicates thatelevated c-di-GMP levels play a negative role in L. monocytogenesvirulence, in an apparent contrast with the role of c-di-AMP.

Materials and Methods

This work was performed in accordance with the recommendations in theGuide for the Care and Use of Laboratory Animals published by theNational Institutes of Health. All procedures were approved by theInstitutional Animal Care and Use Committee (IACUC) at the University ofKentucky (permit number A-3336-01).

Bacterial Strains, Plasmids and Growth Conditions

The bacterial strains and plasmids used in this study are listed inTable 1. The primers used in this study are listed in Table 2. E. coliwas routinely grown in LB medium supplemented with appropriateantibiotics at 25, 30 or 37° C., as indicated. L. monocytogenes wasgrown in Brain Heart Infusion (BHI) medium (Difco), HTM (minimal mediumcontaining 3% glucose) or LB, supplemented with appropriate antibioticsat 25, 30, 37, or 42° C., as indicated.

TABLE 1 Strains and plasmids used in this Example (Table discloses“GGDEF” and “His₆” as SEQ ID NOS 3 and 4, respectively) Strain andplasmid Relevant genotype or description Strains Escherichia coli DH5αStrain used for plasmid maintenance and overexpression of MBP-fusionsBL21(DE3) pLysS Strain used for overexpression of the His₆-fusionsMG1655 Wild type MG1655 ΔyhjH MG1655 ΔyhjH::Km^(r) Listeriamonocytogenes EGD-e Wild type ΔdgcAB In-frame deletion of the dgcABgenes ΔdgcC In-frame deletion in dgcC ΔdgcA/B/C Deletion of the dgcABand dgcC genes ΔpdeB In-frame deletion in pdeB ΔpdeC In-frame deletionin pdeC ΔpdeD In-frame deletion in pdeD ΔpdeB/C Deletion of the pdeB andpdeC genes ΔpdeB/D Deletion of the pdeD and pdeB genes ΔpdeC/D Deletionof the pdeD and pdeC genes ΔpdeB/C/D Deletion of the pdeB, pdeC and pdeDgenes ΔpdeB/C/D ΔpssC ΔpdeB/C/D and in-frame deletion in pssC ΔpdeB/C/DΔpssE ΔpdeB/C/D and in-frame deletion in pssE ΔpdeB/C/D::pIMKΔpdeB/C/D::pIMK2 ΔpdeB/C/D::yhjH ΔpdeB/C/D::(pIMK2::yhjH) ΔpdeB/C/D::slrΔpdeB/C/D::(pIMK2-slr1143) WT::pIMK EGD-e::pIMK2 WT::slrEGDe::(pIMK2::slr1143) WT::yhjH EGDe::(pIMK2::yhjH) PlasmidspBAD/Myc-His-C Vector for arabinose-inducible expression pBAD-dgcApBAD::dgcA pBAD-dgcB pBAD::dgcB pBAD-dgcC pBAD::dgcC pET23a Vector forT7-inducible His₆-fusion protein overexpression pET-pdeD pET23a::pdeDpET-pdeB pET23a::pdeB pET-pdeC pET23a::pdeC pIMK2 L. monocytogeneschromosome integrated expression vector pIMK::slr pIMK2::slr1143pIMK::yhjH pIMK2::yhjH pKSV7 Vector for gene replacements in L.monocytogenes pKSV7-ΔdgcAB Plasmid for in-frame deletion of dgcABpKSV7-ΔdgcC Plasmid for in-frame deletion of dgcC pKSV7-ΔpdeB Plasmidfor in-frame deletion of pdeB pKSV7-ΔpdeC Plasmid for in-frame deletionof pdeC pKSV7-ΔpdeD Plasmid for in-frame deletion of pdeD pKSV7-ΔpssCPlasmid for in-frame deletion of pssC pKSV7-ΔpssE Plasmid for in-framedeletion of pssE pLysS Lysozyme expressing plasmid for T7-expressionsystems pMAL-c2x Vector for MBP-fusion protein overexpression pMAL-pdeCpMAL-c2x::pdeC pMAL-GGDEF_(pssE) pMAL-c2x::pssE(GGDEF domain)

Plasmid and Mutant Construction

Genomic DNA of L. monocytogenes EGD-e was purified from bacterial cellsusing a Bactozol kit. L. monocytogenes genes were PCR amplified usinggenomic DNA, Vent DNA polymerase, and gene-specific primers (Table 5).PCR fragments were gel purified with the Gel Purification kit, digestedwith the appropriate restriction enzymes, and cloned into vectorpMAL-c2x in strain DH5α or into vector pET23a in strain BL21 containingpLysS.

In-frame deletions in the pdeB/C/D, dgcA/B/C, pssC, and pssE genes weregenerated by site-directed mutagenesis by splice-by-overlap extensionPCR. The PCR products containing genes with in-frame deletions werecloned into the temperature-sensitive shuttle vector pKSV7. Therecombinant sequences were used to replace the corresponding wild typesequences in the chromosome of the L. monocytogenes EGD-e strain byallelic exchange. L. monocytogenes was electroporated.

Motility and Congo Red Dye Binding Assays

Briefly, for the analysis of swimming in semi-solid agar, 2 μl ofovernight cultures was inoculated onto soft agar plates containing 0.25%agar, 1% tryptone, and 0.5% NaCl. Diameters of the swimming zones wereassessed after 6-h incubation at 37° C. for E. coli and 12-18-hincubation at 30° C. for L. monocytogenes.

For Congo red binding assays, LB (E. coli) or BHI (L. monocytogenes)agar plates containing 40-80 μg ml⁻¹ Congo red were incubated at 30° C.for 48-72 h.

Biofilm Assays

Surface-adhered biofilm formation was assayed in a 96-well format usinga modified version of a previously published protocol. Briefly,overnight cultures grown in BHI at 30° C. (A₆₀₀, 2.5-3.5) were dilutedinto freshly made BHI, LB or LB supplemented with 3% glycerol to aninitial A₆₀₀ of 0.05-0.1, and 150 μl aliquots of each culture wereinoculated into each of six wells. Biofilms attached to wells weremeasured following growth for 1-6 days at 30° C. Biofilms were stainedwith a 0.1% aqueous solution of Crystal violet dye, which wassubsequently dissolved in 33% acetic acid and quantified by measurementof A₅₉₅.

Protein Overexpression and Purification

For purification of PdeB::His6 (“His₆” disclosed as SEQ ID NO: 4) andPdeD::His₆ (“His₆” disclosed as SEQ ID NO: 4),isopropyl-β-D-thiogalactopyranoside (IPTG) (final concentration, 0.2 mM)was added to exponentially (A₆₀₀, 0.6-0.7) growing cultures of E. coliBL21 (DE3) pLysS containing appropriate overexpression plasmids. After 2to 4 h of induction at 30° C., the cells were chilled to 4° C. andcollected by centrifugation. The cell pellets were resuspended in buffer(pH 8.0) containing 300 mM NaCl, 50 mM NaH₂PO₄, and 10 mM imidazole andprotease inhibitors (phenylmethylsulfonyl fluoride and P8849 proteaseinhibitor cocktail). The cell suspensions were passed through a Frenchpress mini-cell, followed by a brief sonication using a Sonifier 250.The crude cell extracts were centrifuged at 15,000×g for 45 min. Solubleprotein fractions were collected and mixed with preequilibrated Ni²⁺resin for 1 h at 4° C., which was placed into a column and extensivelywashed with the resuspension buffer containing 20 mM imidazole. Theproteins were subsequently eluted using 200 mM imidazole. The buffer wasexchanged with PDE buffer using desalting columns according to theinstructions of the manufacturer. Protein purity was assessed bySDS-PAGE and protein concentration was determined using a BCA proteinassay kit.

For purification of MBP::PdeC and MBP::GGDEF_(pssE) fusions (“GGDEF”disclosed as SEQ ID NO: 3), IPTG (final concentration, 0.2 mM) was addedto exponentially (A₆₀₀, 0.6-0.8) growing E. coli DH5α containingappropriate plasmids. After 2-h induction, cells were collected bycentrifugation. Cell pellets were resuspended in a buffer containing 200mM NaCl, 0.5 mM EDTA, 5 mM MgCl₂, 20 mM Tris-HCl (pH 7.6), and 5%glycerol that also contained protease inhibitors. Following celldisruption and clearing of the crude cell extracts, as described above,soluble protein fractions were mixed with pre-equilibrated amylose resinfor 1 h at 4° C., which was subsequently extensively washed with theresuspension buffer. MBP fusions were eluted with maltose and the bufferwas exchanged for PDE or c-di-GMP binding assay buffer using desaltingcolumns.

PDE Assays

Briefly, assays were performed by adding a PDE enzyme (1-5 μM) to PDEreaction buffer (final volume, 100 μl) containing 250 μM c-di-GMP, andthe reaction was allowed to proceed at 37° C. Aliquots were withdrawn atvarious time points; the reaction was stopped by addition of CaCl₂(final concentration, 10 mM), and the sample was boiled for 3 min andcentrifuged. The supernatant was then filtered through a 0.22-μm filter,and the reaction products were analyzed by reversed-phase HPLC using aSupelcosil LC-18-T column. The buffer system and gradient elutionprogram were described previously.

Equilibrium Dialysis

Equilibrium dialysis experiments were performed as previously described.Briefly, MBP-GGDEF_(PssE) (“GGDEF” disclosed as SEQ ID NO: 3) (20 μM)was injected into one of the two chambers of a Dispo-Biodialyzercassette (10 kD cutoff) filled with dialysis buffer. c-di-GMP(concentrations from 1 to 50 μM) was injected into the opposite cell ofthe cassette. The cassettes were maintained for 25 h at room temperatureunder agitation, after which samples from each chamber were withdrawn,boiled for 3 min, centrifuged, and supernatants were filtered through a0.22-μm microfilter. The nucleotide concentrations were quantified byHPLC. Binding constants were calculated by the GraphPad Prism software,version 4.03 using a nonlinear regression model.

Invasion Assay

L. monocytogenes invasion properties were analyzed using agentamicin-based assay with HT-29 human colon adenocarcinoma cellmonolayers in 24-well plates. Briefly, overnight cultures of L.monocytogenes grown in BHI at 37° C. were centrifuged, washed, andresuspended in DMEM medium. Monolayers of HT-29 cells were inoculatedwith 100 μl of the L. monocytogenes suspensions (˜5×10⁸ CFU ml⁻¹) at amultiplicity of infection of 100 and incubated for 1.5 h at 37° C. in a7% CO₂ atmosphere. The monolayers were then washed and incubated in thepresence of 100 μg gentamicin ml⁻¹ (final concentration) for 1.5 h.Following this incubation, the cell monolayers were washed again andlysed with 0.1% Triton X-100. Appropriate dilutions were plated on BHIplates for enumeration of intracellular bacteria. Each experiment wasdone in triplicate, and experiments were performed at least three timesindependently. Statistical analysis was performed by using Tukey's testat p of <0.05.

Foodborne Infection of Mice

Female BALB/c/By/J mice were purchased from The Jackson Laboratory at 5weeks of age and used in experiments when they were 6-9 weeks old. Micewere maintained in a specific pathogen free facility at the Universityof Kentucky and all procedures were performed in accordance with IACUCguidelines. Aliquots of early stationary phase bacteria were preparedand stored at −80° C. To prepare the inoculum, aliquots were thawed onice, cultured standing in BHI broth for 1.5 h at 30° C., washed once inPBS and then suspended in 5 μl of melted, salted butter and used tosaturate a 2-3 mm piece of white bread. Infection by the natural feedingroute was carried out at night. Briefly, mice were given unrestrictedaccess to water but denied food for 22 h, then placed in an empty cage,and given 5-10 minutes to pick up the contaminated bread piece and eatall of it. Mice were then returned to their original cages with raisedwire flooring to prevent coprophagy, and normal mouse chow wasreplenished.

Processing of Tissue Samples

Colon contents were removed by squeezing with sterile forceps and thenflushing with 8 ml of PBS through a 25 g needle. Washed tissues were cutlongitudinally and homogenized for 1 min in 2 ml of sterile water usinga PowerGen 1000 homogenizer at 60% power. The total number ofcell-associated (adherent plus intracellular) L. monocytogenes cells wasdetermined by plating serial dilutions on BHI agar supplemented with 15g LiCl l⁻¹ and 10 g glycine l⁻¹ (BHI/L+G). Colonies were counted after48 h incubation at 37° C. This selective agar inhibited the growth ofmost intestinal microbiota; suspect colonies were confirmed to be L.monocytogenes by plating on CHROMagar Listeria plates. Spleens andlivers were harvested aseptically and homogenized for 30 sec in 2 ml ofsterile water. Gallbladders were ruptured with sterile scissors in amicrofuge tube containing 1 ml of sterile water and vortexed for 30 sec.Dilutions of each tissue were plated on BHI/L+G agar.

Disinfection and Desiccation Tolerance

Solutions of sodium hypochlorite, hydrogen peroxide, and benzalkoniumchloride were prepared in sterile phosphate-buffered saline withdisinfection concentrations of 1600 ppm, 200 mM, and 100 ppm,respectively. Cultures were grown in HTM with 3% glucose at 37° C. for24 h, at which point small uniform clumps are formed by the ΔpdeB/C/Dstrain. Aliquots (250 μl; 10⁸ cfu/ml) of these cultures were mixed withdisinfectants at 1:1 vol ratios in small glass tubes that also contained0.1 g of acid washed glass beads. Following a 10-min exposure todisinfectants at room temperature, D/E neutralizing broth (500 μl) wasadded. Samples were vigorously vortexed for 5 min. and clumps of theΔpdeB/C/D strain were dispersed due to the action of the glass beads.Serial dilutions were plated on BHI agar and colonies were countedfollowing a 48-h incubation at 37° C.

To assess desiccation tolerance, strains were grown as described above.One milliliter of cultures (5×10⁸ cfu/ml) was centrifuged in 1.5 mleppendorf microtubes containing 0.1 g glass beads. After supernatantremoval, the tubes were stored at room temperature in a desiccator jarcontaining anhydrous calcium sulfate. After 7 and 21 days, the pelletswere resuspended in phosphate buffered saline, vigorously vortexed, andplated on BHI agar. Colonies were counted following 48-h incubation at37° C.

Example II

Elevated levels of the second messenger c-di-GMP activate biosynthesisof an exopolysaccharide (EPS) of previously unknown composition in thefood-borne pathogen Listeria monocytogenes. This EPS protects cellsagainst disinfectants and desiccation, indicating its significance forlisterial persistence in the environment and for food safety. Thephylogenetic origin of this EPS was analyzed, its composition wasdetermined, the genes involved in its biosyntehsis and hydrolysis werecharacterized and and diguanylate cyclases activating its synthesis wereidentified. Phylogenetic analysis of EPS biosynthesis proteins indicatesthey have evolved within monoderms. Scanning electron miscroscopyrevealed that L. monocytogenes EPS is cell surface-bound. Secretedcarbohydrates represent exclusively cell-wall debris. The purified EPShas a unique composition, i.e., N-acetylmannosamine (ManNAc) andgalactose (Gal) in a 2:1 ratio. Linkage analysis revealed 4-ManNac,4,6-ManNAc, and terminal-Gal residues. All genes of the pssA-E operonare required for EPS production and so is a separately located pssZgene. The examples show that PssZ has an EPS-specific glycosylhydrolaseactivity. The exogenously added PssZ prevents EPS-mediated cellaggregation and disperses preformed cell aggregates, whereas the E72Qmutant in the presumed catalytic residue, is much less active. Thediguanylate cyclases DgcA and DgcB, whose genes are located next topssZ, are dedicated to EPS regulation.

All L. Monocytogenes pssA-E Operon Genes are Required for Biosynthesisof Cell-Bound EPS

The L. monocytogenes ΔpdeB/C/D mutant, in which all c-di-GMPphosphodiesterase (PDE) genes are deleted, and therefore intracellularc-di-GMP levels are expected to be elevated compared with the wild type,produces copious amounts of EPS in minimal HTM medium with 3% glucose(HTM/G). This EPS is responsible for aggregation of the ΔpdeB/C/D strain(FIG. 9A), which indicates that at least some EPS is cell bound.Therefore, attempts to visualize it via scanning electron microscopy(SEM) were made. Intercellular fiber-like connections between ΔpdeB/C/Dcells were observed, whereas no intercellular connections were seen withthe EPS-negative ΔpdeB/C/D ΔpssC strain containing a deletion of theglycosyltransferase gene, or in the wild-type strain, EGD-e (FIGS.9A-9C). The cell surface-attached EPS synthesized by ΔpdeB/C/D cellsapparently accounts for the formation of large cell aggregates in HTM/Gmedium. These aggregates settle out from the culture medium whenflasks/test tubes are not agitated. The aggregates are not easilydispersed by vortexing but can be dispersed by vortexing in the presenceof glass beads. Following dispersion, the aggregates do not reform.

Two genes of the pssA-E operon, pssC and pssE, are indispensable for EPSbiosynthesis. In order to test the involvement of other pss genes,in-frame deletions in the remaining genes of this operon (FIG. 10A) wereconstructed and used cell aggregation in HTM/G liquid medium and Congored dye binding in HTM/G agar medium to assess EPS production. As shownin FIGS. 10B-10C, deletions in pssA, pssB and pssD in the ΔpdeB/C/Dgenetic background abrogated both phenotypes, thereby indicating thatall pssA-E genes are involved in listerial EPS biosynthesis.

The Listerial EPS Biosynthesis Machinery has Evolved within Monodermsand the Listerial EPS has a Unique Composition

The PssC and glycosyltransferases involved in cellulose and PNAGbiosynthesis are approximately similar. The PssD and the BcsB proteins(Pfam protein domain: BcsB), which have thus far been associatedexclusively with cellulose synthases, are also approximately similar.Phylogenetic analysis of key listerial EPS biosynthetic proteins wereconducted. Phylogenetic trees were constructed for PssC, PssD, and PssZ(an EPS-specific glycosylhydrolase). It was found that sequences ofthese three listerial proteins clustered within a branch of Firmicutes(and include homologs from Bacillus, Clostridium, and Lactobacillus) andare closer related to proteins from Actinobacteria and/or Greenfilamentous bacteria, sister monoderm (single-membrane bacteria)branches, to the exclusion of proteobacterial sequences (FIGS. 11A-11C).

Comparative genomic analysis identified gene clusters in other Listeriaspecies (e.g. L. innocua, L. seeligeri and L. ivanovii), bacilli,including the model firmicute Bacillus subtilis (ydaJ-ydaN), andclostridia, including the emerging pathogen Peptoclostridium difficile(CD630_10280-D630_10310), which are homologous to the listerial pssoperon. Therefore, listerial EPS biosynthesis proteins have evolvedwithin monoderms rather than being acquired via horizontal gene transferfrom other branches such as the proteobacteria. This analysis indicatesthat the composition of the listerial EPS is unique and unrelated toPNAG or cellulose.

The c-di-GMP-Activated L. Monocytogenes EPS is Composed of ManNAc andGal

To purify the cell-bound EPS, the ΔpdeB/C/D strain was used, whereas theΔpdeB/C/D ΔpssC mutant impaired in the EPS synthesis was used as anegative control. The cell-bound EPS was removed from cells by boilingfollowed by ethanol precipitation. The insoluble cell-bound EPS wasisolated from the ΔpdeB/C/D strain but not from the ΔpdeB/C/D ΔpssCstrain. This EPS contained carbohydrates, based on the anthronereaction, but was not affected by cell-wall hydrolases (lysozyme andmutanolysin) or nucleases (DNase I and RNase A).

Glycosyl composition analysis performed at the Complex CarbohydrateResearch Center showed that the purified listerial EPS is made ofN-acetylmannosamine (64.9%) and galactose (33.6%) (Table 2). Thepreparation also contains trace amounts of other sugars (1.4% of itsmolar mass) that are unlikely to be genuine components of the polymer.Linkage analysis demonstrated the pyranose forms of terminal galactose(t-Galp), 4-linked N-acetyl mannosamine (4-ManpNAc), and 4,6-linkedN-acetyl mannosamine (4,6-ManpNAc). Based on the presence ofN-acetylmannosamine in approximately twofold abundance over terminalgalactose, listerial EPS consists of a heteropolymer with atrisaccharide repeat unit of{4)-ManpNAc-(1-4)-[Galp-(1-6)]-ManpNAc-(1-}, which is referred to hereinas ManNAc-Gal EPS (FIG. 12). To confirm this repeat unit and determinethe configurations of the linkages between ManNAc and galactoseresidues, the structure of ManNAc-Gal EPS was analyzed by NMRspectroscopy.

TABLE 2 Monosaccharide composition of L. monocytogenes EPS Glycosylresidue Mass (μg) Mol % Rhamnose (Rha) 1.2 0.4 Mannose (Man) 0.8 0.3Galactose (Gal) 102.2 33.6 Glucose (Glc) 2.2 0.7 N-acetyl mannosamine(ManNAc) 242.3 64.9 Sample carbohydrate content, Σ 348.7 99.9

Identification and Chemical Shift Assignment of Monosaccharide Residuesin ManNAc-Gal EPS

The ManNAc-Gal EPS was completely insoluble, precluding liquid-state NMRanalysis on the native material. Considering that chitin, a polymer ofβ-1,4-linked N-acetylglucosamine, is also insoluble, but chitosan, whichis obtained from chitin by N-deacetylation, is soluble in dilute acid,ManNAc-Gal EPS may also be made soluble by N-deacetylation. Sodiumhydroxide treatment of ManNAc-Gal EPS removed about 80% of N-acetylgroups (estimated by integration of the acetyl-CH₃ signal at 2.08 ppm)and resulted in EPS-N, which was freely soluble in dilute acid. The 1-Dproton NMR spectrum of EPS-N (FIG. 13A) showed two broad, partiallyoverlapping anomeric signals at a chemical shift above 5 ppm and severalbroad peaks between 4.2 and 3.7 ppm. To identify the sugars belonging tothe anomeric signals, a series of 2-D NMR spectra was acquired. COSY andTOCSY spectra were used to assign the proton chemical shifts, and anHSQC spectrum was obtained to assign the carbon chemical shifts of themonosaccharide residues present in EPS-N. The residues and their linkagepositions were identified from the proton and carbon chemical shifts. ANOESY spectrum was used to determine the monosaccharide sequence. Thespectra clearly identified one of the anomeric peaks as belonging to aterminal α-galactopyranose (α-Galp) residue (Table 3).

TABLE 3 NMR chemical shifts of N-deacetylated listerial EPS Chemicalshift (ppm) Sample Residue 1 2 3 4 5 6 EPS-N A 4,6-β-ManN•HCl 5.115 3.984.21 3.95 3.89 3.98/3.86

   56.8 70.6

76.1

B 4-β-ManN•HCl 5.106 3.97 4.19 3.91 3.70 3.93/3.80

   56.8 70.7

77.7 62.9 C α-Gal 5.080 3.89 3.90 4.00 3.88 3.78/3.76

   70.9 72.3 72.0 74.1 64.1 EPS-H A′ 4,6-β-ManN•HCl 5.113 3.98 4.21 3.953.91 3.99/3.86

   56.8 70.6

76.3

(168 Hz) B′ 4-β-ManN•HCl 5.096 3.97 4.20 3.92 3.71 3.94/3.80

   56.8 70.7

77.6 62.9 (168 Hz) C′ α-Gal 5.076 3.89 3.90 4.00 3.88 3.78/3.76

   70.9 72.3 72.0 74.1 64.1 (172 Hz) Monosaccharide α-ManN•HCl 5.40 3.68 4.17 3.61 3.92 3.84/3.83 Standards 93.1   57.2 69.5 69.0 74.7 63.1(171 Hz) β-ManN•HCl 5.20  3.72 4.01 3.54 3.47 3.90/3.76 93.7   58.3 72.168.8 78.8 63.2 (167 Hz) Carbon chemical shifts are in italics; downfieldcarbon shifts indicating glycosylation are in bold. Measured ¹J_(CH)coupling constants are in parentheses.

The residue to which the second anomeric signal belonged was difficultto identify due to spectral overlap. However, the signals that could beobserved were consistent with mannosamine hydrochloride (ManpN.HCl). Inorder to obtain a complete assignment of the mannosamine residues, EPS-Nwas subjected to to partial acid hydrolysis (obtaining EPS-H). The 1-Dproton NMR spectrum of the resulting EPS-H confirmed that the galactoseside chains were cleaved more readily than the mannosamine backbone,showing considerable reduction of the galactose anomeric proton signal(FIG. 13A), as well as complete loss of residual N-acetyl groups. The2-D NMR analysis of EPS-H allowed the chemical shifts of the mannosamineresidues to be completely assigned. These chemical shifts wereidentified as 4-linked, based on the downfield chemical shift of C4(Table 3). The spectra of EPS-H still showed a minor amount ofα-galactose, and therefore a branching mannosamine residue to which thegalactose is attached (FIG. 13A) was also seen. The linkage data of thenative EPS had shown the presence of 4,6-linked mannosamine, and as thebackbone was 1→4-linked, branching was seen on O-6 of mannosamine. TheHSQC spectrum (FIG. 13B) displayed a weak set of CH₂ signals at 68.7ppm, exhibiting downfield displacement typical of glycosylation andindicating the residual presence of 4,6-linked mannosamine. Similarsignals were present in the HSQC spectrum of EPS-N where they had aboutequal intensity with those from 4-linked mannosamine (FIG. 13B),indicating that branching occurs on every other mannosamine residue. Inaddition to identifying the H/C-6 mannosamine signals, the comparison ofthe spectra of EPS-N with those from EPS-H allowed the assignment of theremaining mannosamine signals in EPS-N, and this assignment issummarized in Table 3. NOESY confirmed the putative sequence bydetecting correlations between the anomeric proton of galactose and H-6of 4,6-ManN, and between the anomeric protons of the ManN residues withH-4 of ManN (FIG. 13C).

Anomeric Configurations of Monosaccharide Residues in ManNAc-Gal EPS

It is difficult to determine the anomeric configuration of sugars withmanno-stereochemistry because the H1-H2 coupling constants and thechemical shifts of both anomers are similar. The anomeric 1-bond C—HJ-coupling constants have been shown to often provide a more unambiguousdistinction between α- and β-configurations of pyranoses andmethylpyranosides. Thus, α-anomeric pyranoses typically have 1JCH valuesbetween 169 and 173 Hz, and β-pyranoses between 158 and 162 Hz. In orderto measure the 1JCH coupling constant of the mannosamine anomeric C—Hpair, an HSQC spectrum of EPS-H without decoupling during acquisitionwas acquired using a narrow spectral width in the carbon dimension,covering only the anomeric carbons (FIG. 14). The 1JCH couplingconstants of the mannosamine residues were 168 Hz, and that of thegalactose residue was 172 Hz, indicating that galactose was in theα-anomeric configuration, but giving no conclusive answer regarding theanomeric configuration of mannosamine. For the galactose residue, thiswas in agreement with the assigned chemical shifts. Although the 1JCHcoupling constant of 168 Hz was closer to the typical range ofα-pyranoses, the chemical shifts of the mannosamine residues seemed toagree better with the β-configuration as C-5 of both of the mannosamineresidues resonated further downfield than would be expected for theα-anomer. Furthermore, the NOESY spectrum reveals NOE contacts of theanomeric proton with H2, H3, H4, and H5 (FIG. 13C), which is onlypossible in the β-anomer. Of these correlations, H1-H2, H1-H3, and H1-H5are with protons of the same residue, whereas the correlation H1-H4reveals a short distance between the anomeric proton and H4 of theneighboring ManN residue.

The 1JCH coupling constants of both anomers of fully acylatedmannosamine have been reported as 178.4 and 166.7 Hz for α and β,respectively. However, O1-acylation increases the anomeric 1JCH couplingconstant by about 5 Hz. No 1JCH coupling constants for α- andβ-mannosamine hydrochloride have been reported previously. In order toobtain these values, mannosamine hydrochloride was synthesized fromN-acetylmannosamine by acid hydrolysis, and sufficient NMR data toassign both α- and β-pyranose anomers and to measure their anomeric 1JCHcoupling constants was acquired. The results are demonstrated in FIG. 14and listed in Table 3, and show that β-ManN.HCl has an unusually large1JCH coupling constant of 167 Hz between C1 and H1. This, together withthe better agreement of the carbon chemical shifts with the β-anomer ofthe standard as well as the multiple NOESY cross peaks, indicates thatthe ManN in the EPS has the β-configuration. The EPS trisacchariderepeating unit structure is therefore as follows:

The Secreted L. Monocytogenes Carbohydrates are pss Independent

Whether some of the listerial EPS is also secreted in the growth medium,in addition to being cell-surface attached, was tested. To extractsecreted carbohydrates, culture supernatants of the ΔpdeB/C/D andΔpdeB/C/D ΔpssC strains, from which cell wall debris, extracellular DNA,and proteins were removed, were used. Soluble carbohydrates wereprecipitated with ethanol. It was found that the re-solubilized ethanolprecipitants derived from culture supernatants of the two strainscontained the same amounts of total carbohydrates (as determined by theanthrone reaction). This result indicates that secreted carbohydrates donot depend on the glycosyltransferase PssC and pss operon.

To further investigate the nature of these secreted carbohydrates, theywere subjected to NMR spectroscopic analyses. The proton NMR spectra inD₂O revealed identical compositions for the secreted carbohydrates fromthe ΔpdeB/C/D and ΔpdeB/C/D ΔpssC strains, which were dominated byrhamnose and N-acetylglucosamine (FIG. 15A). The identity of sugarresidues was confirmed by 2D proton TOCSYNMR (FIGS. 15B-15D). Becauserhamnose and N-acetylglucosamine are abundant in teichoic acids instrain EGD-e and in the peptidoglycan, and because PssC does not affectthe abundance of extracellular soluble carbohydrates, the conclusion isthat they are derived from the L. monocytogenes cell-wall debris and areunrelated to the ManNAc-Gal EPS. Hence, ManNAc-Gal EPS is producedexclusively in an insoluble, cell surface-attached form.

Genetic Evidence that pssZ (lmo1913) Encodes a ManNAc-Gal EPS-SpecificGlycosylhydrolase

The pss operon lacks an identifiable gene for a ManNAc-Gal EPS hydrolasenecessary for EPS processing. It was previously noticed that the lmo1913gene located in the gene cluster involved in c-di-GMP synthesis anddegradation, dgcA-dgcB-lmo1913-pdeC (FIG. 16A), encodes a putativeglycosylhydrolase. In this operon, dgcA and dgcB encode DGC enzymes andpdeC encodes a c-di-GMP PDE.

To test whether lmo1913 encodes a ManNAc-Gal EPS-specificglycosylhydrolase, lmo1913 was overexpressed in the ΔpdeB/C/D strain byintegrating an additional copy of lmo1913 downstream of a strongpromoter in the chromosome (strain ΔpdeB/C/D-pssZ, Table 3).Overexpression of the lmo1913 gene did not change Congo red bindingsignificantly; however, it reduced cell aggregation in liquid HTM/Gmedium (FIGS. 16B and 16C, strains 1 and 5; FIG. 16D). The deletion ofthe wild-type lmo1913 gene in the ΔpdeB/C/D background (strain ΔpdeB/C/DΔpssZ) drastically reduced Congo red binding and abolished cellaggregation (FIGS. 16B-16C, strains 1 and 2). These observations areconsistent with the EPS glycosylhydrolase function of Lmo1913, which isherein designated PssZ [in accord with other glycosylhydrolases, e.g.BcsZ]. Notably, the ΔpdeB/C/D ΔpssZ strain was not impaired inManNAc-Gal EPS synthesis and produced some ManNAc-Gal EPS, which can beinferred from its higher Congo red staining, compared with the stainingof EGD-e and the EPS negative ΔpdeB/C/D ΔpssC strain (FIG. 16B, strains2, 6, and 7). These results indicate that PssZ is not essential forManNAc-Gal EPS biosynthesis but is necessary for optimal ManNAc-Gal EPSproduction.

Biochemical Evidence that PssZ has ManNAc-Gal EPS-SpecificGlycosylhydrolase Activity

To test the ManNAc-Gal EPS-specific glycosylhydrolase activity of PssZmore directly, a fragment of this protein lacking the transmembranedomain but retaining the presumed catalytic domain was overexpressed inE. coli and purified as a C-terminal His6-fusion (“His6” disclosed asSEQ ID NO: 4) (FIG. 17A). In addition, the PssZ point mutant E72Q, whichis believed to be impaired in hydrolytic activity, was constructed andpurified (FIG. 17A). As shown in FIG. 9B, Glu72 is conserved in PssZ andits homolog from the bacterial species L. innocua, and is also conservedamong other members of the glycosylhydrolase family 8, to which PssZ maybelong. The complementation of the ΔpdeB/C/D ΔpssZ strain with thewild-type pssZ gene (strain ΔpdeB/C/D ΔpssZ-pssZ) restored Congo redbinding and cell aggregation phenotypes, whereas complementation withpssZ E72Q (strain ΔpdeB/C/D ΔpssZ-pssZ E72Q) failed to do so (FIG.16B-16C, strains 2, 3, and 4).

Next, purified insoluble ManNAc-Gal EPS was treated with PssZ and PssZE72Q. The anthrone assay did not detect any PssZ activity, indicatingthat PssZ is not able to solubilize and hydrolyze ethanolprecipitatedEPS. However, the addition of purified PssZ to the inoculum of theΔpdeB/C/D strain inhibited cell aggregation in a dose-dependent manner,i.e., 0.13 μg ml⁻¹ (final concentration) inhibited aggregationpartially, whereas a 10-fold higher level of PssZ (1.3 μg ml⁻¹)inhibited it completely (FIG. 17C). When purified PssZ E72Q was testedin the same assay, it had only a minimal effect on cell aggregationpossibly due to its residual hydrolytic activity (FIG. 17C). Theseresults indicate that PssZ hydrolyzes listerial EPS.

Whether PssZ can disperse preformed cell aggregates of the ΔpdeB/C/Dstrain was also tested. Cell aggregates from a stationary phase culturewere mixed with the PssZ and PssZ E72Q proteins in medium containing HTMsalts lacking a carbon source and incubated at 30° C. PssZ (32 μg ml⁻¹,final concentration) dispersed cell aggregates almost completely after 6h of incubation (FIG. 17D), whereas PssZ E72Q, used at the sameconcentration, decreased cell aggregates to a much lesser degree (FIG.17D). The presence of reducing sugars in the supernatants obtained aftertreatment of cell aggregates with the wild-type PssZ protein was able tobe detected. These results show that PssZ is a ManNAc-Gal EPS-specificglycosylhydrolase.

Contributions of Listerial DGCs to ManNAc-Gal EPS Biosynthesis

Given that the pssZ gene is located next to the dgcA and dgcB genesencoding DGCs, it was questioned whether these dgc genes were primarilyresponsible for stimulating ManNAc-Gal EPS biosynthesis. To analyze therole of these DGCs in EPS production, individual in-frame deletions wereconstructed in dgcA and dgcB, as well as a deletion in both genes in theΔpdeB/C/D mutant background. A deletion in the third DGC gene present inL. monocytogenes, dgcC, was also constructed for comparison. Deletionsof either dgcA or dgcB genes drastically decreased Congo red binding aswell as cell aggregation in HTM/G liquid medium (FIGS. 181-18C).Deletion of both genes resulted in a more severe defect in cellaggregation than the individual deletions, although this was not aspronounced in the Congo red binding assay. In contrast, deletion of thedgcC gene did not decrease Congo red binding (FIG. 18A) or cellaggregation (FIG. 18B and FIG. 18C). Therefore, DgcA and DgcB are thetwo DGCs primarily responsible for regulating ManNAc-Gal EPS synthesis.

Discussion

The ability of L. monocytogenes to produce EPS has been controversialfor a long time. Indirect evidence of EPS production by variouslisterial strains has been previously demonstrated using varioustechniques, e.g. staining with ruthenium red and Congo red,fluorescein-conjugated lectin binding, fluorescent dye-conjugatedantibody binding, phenolic sulfuric acid analysis, and fibril or matrixanalysis via SEM. Earlier, a putative EPS biosynthesis clusterresponsible for Congo red binding and cell aggregation, as well asdrastically increased tolerance of L. monocytogenes to commonly useddisinfectants and to desiccation, was identified. It was also shown thatEPS biosynthesis is activated by c-di-GMP via the I-site c-di-GMPreceptor PssE. This example elucidates the relationship betweenlisterial EPS and other EPSs, the composition and structure of listerialEPS, the genes involved in the synthesis and hydrolysis of listerialEPS, and the DGCs involved in c-di-GMP-dependent regulation of EPSbiosynthesis.

It was determined that listerial EPS produced by the pssA-E operonproteins is exclusively cell bound, as carbohydrates secreted in culturemedia contained sugars characteristic of cell-wall material, and theirquantities were independent of the glycosyltransferase PssC. Thelisterial EPS has a unique structure. Based on composition, linkage, andNMR analysis, listerial EPS is a heteropolymer with a trisacchariderepeat unit consisting of{4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}. This structuralanalysis provides extra information indicating that theglycosyltransferase PssC belongs to the glycosyl hydrolase family 2proteins, which utilize an inversion mechanism during polymerization ofactivated sugar residues (in this case, UDP-α-ManNAc). The resultingpolymer synthesized by PssC therefore contains β1-4 linked ManNAcresidues. Finally, the ManNAc-Gal EPS structure is further supported bythe sequence information of the dedicated glycosylhydrolase PssZ thatbelongs to the class of β1-4 linkage-specific glycosylhydrolases.

The phylogenetic analyses (FIGS. 11A-11C) indicate that ManNAc-Galbiosynthesis has evolved in monoderms, rather than being recentlybrought in by a horizontal gene transfer, as supported by thesimilarities of PssC to cellulose and PNAG synthases from theproteobacteria, and the similarity of PssD to the BcsB protein. It isnoteworthy that BcsB has previously been found to be associated onlywith cellulose biosynthesis. The recent structure of the cellulosesynthase from R. sphaeroides showed that BcsB facilitates movement ofthe growing cellulose chain through the cell wall and periplasmic space.Without wishing to be bound by theory, it is believed that PssD performsa similar function in ManNAc-Gal EPS extrusion through the cell wall.Therefore, the BcsB domain present in the BcsB and PssD proteins initself is not specific toward a given polysaccharide; instead, it formsan EPS extrusion scaffold.

The functions of the PssA and PssB proteins encoded in the pss operonare less clear, although, as we determined here, all of them arerequired for ManNAc-Gal EPS synthesis. Although the function of PssAcannot be predicted, the PssB protein seems to belong to thecarbohydrate esterase 4 superfamily that contains enzymes performingdeacetylation of chitin, peptidoglycan, and xylan. Therefore, it isbelieved that PssB deacetylates some of the ManNAc residues in thelisterial EPS. Such residues would not have been detected in thelisterial EPS due to the methodology used to determine itsmonosaccharide composition. Surprisingly, deletion of PssB, which isbelieved to be nonessential, abolished ManNAc-Gal EPS synthesis. Withoutwishing to be bound by theory, it is believed that this occurs due to arequirement for the PssB protein (and perhaps PssA) for assembly of theEPS biosynthetic machinery. Similar to this observation, PelA, whichalso belongs to the carbohydrate esterase 4 superfamily, is necessaryfor Pel biosynthesis by P. aeruginosa. One enzyme critical forManNAc-Gal EPS synthesis that so far has escaped identification is theα-galactosyl transferase that decorates the ManNAc chain.

In addition to biosynthesis proteins, the ManNAc-Gal EPS-specificglycosylhydrolase was identified and characterized. PssZ belongs to theGH8 family, whose members cleave β1-4 linkages through an invertingmechanism wherein carboxylate containing amino acid residues (i.e., Gluand Asp) perform the hydrolysis of glycosidic bonds. A conserved Gluresidue present in the presumed catalytic site of PssZ was identified tobe important for hydrolytic activity of PssZ (FIG. 17). The PssZ E72Qmutation largely, but not completely, abolished hydrolytic activity.This finding is consistent with the outcomes observed for mutations madein the similarly positioned Glu residues in the active sites of thecellulase BcsZ and endoglucanase K. This example also shows thatexogenously added PssZ protein prevents listerial aggregation anddisperses preformed cell aggregates (FIG. 17) but is inactive towardpurified insoluble ManNAc-Gal EPS. A similar observation was reportedfor BcsZ, i.e., no hydrolytic activity was detected oncarboxymethylcellulose in solution, whereas activity was shown on anagar plate containing carboxymethylcellulose. The soluble fragment ofPssZ retains partial hydrolytic activity after 3 day incubation at 30°C. Given its relative stability, PssZ can be used for dispersinglisterial EPS aggregates in food storage or processing plants, whichwould make listeria more susceptible to disinfectants. According to theresults observed, listerial EPS-embedded aggregates are several ordersof magnitude more tolerant to commonly used disinfectants thanplanktonic cells.

Without wishing to be bound by theory, it is believed ManNAc-Gal EPSbiosynthesis in L. monocytogenes occurs according to the modelillustrated in FIG. 19. According to this model, an unknown signal(s)induces the DGC activity of DgcA and/or DgcB, which may be physicallyassociated with the Pss biosynthetic machinery. The locally generatedc-di-GMP binds to the PssE receptor and stabilizes the PssE-PssC complexin a catalytically favorable conformation for ManNAc-Gal EPS synthesis.The c-di-GMP PDE, PdeC, possibly together with other PDEs, preventsnonspecific activation of the EPS synthesis via DgcC. During EPSsynthesis, PssD assists the movement of the growing polysaccharide chainonto the cell surface, similar to the BcsB subunit of cellulosesynthases. PssB may modify EPS through deacetlylation, whereas PssZperiodically cleaves the ManNAc-Gal EPS chain to facilitate anunobstructed extrusion of the polymer and hydrolyzes it more rigorouslyfor bacterial escape from aggregates.

Experimental Procedures

Bacterial Strains, Plasmids, and Growth Conditions

Bacterial strains, plasmids and their characteristics are listed inTable 4. L. monocytogenes EGD-e and derivatives of this strain wereaerobically grown in brain hearth infusion (BHI) broth (Difco) withappropriate antibiotics, when needed, at 37° C. Escherichia coli DH5α(Invitrogen), S17-1 and BL21 (DE3) pLysS (Invitrogen) were used forcloning, conjugation, and protein purification experiments,respectively. These strains were routinely cultured in Luria-Bertanibroth (LB) (Difco) with appropriate antibiotics. pKSV7, pIMK2, andpET23a vectors were used for construction of in-frame deletions in L.monocytogenes, protein overexpression in L. monocytogenes, and proteinpurifications in E. coli, respectively.

TABLE 4 Strains and plasmids used in this example (“His6” disclosed asSEQ ID NO: 4) Strain or plasmid Description Strains Escherichia coliDH5α Strain for plasmid construction and maintenance S17-1 Strain forconjugative transformation of L. monocytogenes strains with pIMK2constructs BL21 [DE3] pLysS Strain for protein purification Listeriamonocytogenes EGD-e Wild-type (WT) ΔpdeB/C/D In-frame deletion of pdeB(lmo0131), pdeC (lmo1914) and pdeD (lmo0111) genes. High c-di-GMP andEPS overproducer ΔpdeB/C/D ΔdgcA In-frame deletion of dgcA in ΔpdeB/C/DΔpdeB/C/D ΔdgcB In-frame deletion of dgcB in ΔpdeB/C/D ΔpdeB/C/D ΔdgcCIn-frame deletion of dgcC in ΔpdeB/C/D ΔpdeB/C/D ΔdgcA/B In-framedeletion of the dgcA-dgcB locus in ΔpdeB/C/D ΔpdeB/C/D ΔpssA In-framedeletion of pssA in ΔpdeB/C/D ΔpdeB/C/D ΔpssB In-frame deletion of pssBin ΔpdeB/C/D ΔpdeB/C/D ΔpssC High c-di-GMP and impaired EPS productionΔpdeB/C/D ΔpssD In-frame deletion of pssD in ΔpdeB/C/D ΔpdeB/C/D ΔpssEHigh c-di-GMP and impaired EPS production ΔpdeB/C/D ΔpssZ In-framedeletion of pssZ in ΔpdeB/C/D ΔpdeB/C/D ΔpssZ-pssZ Complementation ofΔpssZ mutation by wild-type pssZ; ΔpdeB/C/D ΔpssZ ::pIMK2::pssZΔpdeB/C/D ΔpssZ-pssZ E72Q Complementation of ΔpssZ mutation by pssZE72Q; ΔpdeB/C/D ΔpssZ ::pIMK2::pssZ E72Q ΔpdeB/C/D-pIMK2 Control strainfor overexpression studies; ΔpdeB/C/D::pIMK2 ΔpdeB/C/D-pssZ Chromosomaloverexpression of PssZ in ΔpdeB/C/D; ΔpdeB/C/D::pIMK2::pssZ PlasmidspET23a Plasmid for His₆ tagged protein purification pET23a-PssZpET23a::pssZ; PssZ-His₆ overexpression plasmid pET23a-PssZ E72QpET23a::pssZ E72Q; PssZ E72Q-His₆ overexpression plasmid pIMK2 Vectorfor chromosomal expression in L. monocytogenes pIMK2-pssZ pIMK2::pssZ;chromosomal complementation with WT PssZ pIMK2-pssZ E72Q pIMK2::pssZE72Q; chromosomal complementation with single amino acid substitutioncopy of PssZ pKSV7 Vector for gene deletion in L. monocytogenespKSV7-ΔpssA Plasmid for in-frame deletion of pssA pKSV7-ΔpssB Plasmidfor in-frame deletion of pssB pKSV7-ΔpssD Plasmid for in-frame deletionof pssD pKSV7-ΔpssZ Plasmid for in-frame deletion of pssZ

Bioinformatics Analysis

According to the Pfam database, L. innocua Lin2027 belongs to the GH8family proteins, whereas PssZ (Lmo1913) is not recognized as a member ofthe GH8 family. In order to detect conserved residues in PssZpotentially involved in catalysis, the consensus sequence of GH8proteins was aligned with the sequences of Lin2027 and PssZ. Thephylogenetic analyses were performed as follows. Seed domain sequenceswere downloaded from phylogenetic trees in the Pfam domain database andaligned with the proteins of interest using Muscle(http://www.ebi.ac.uk/Tools/msa/muscle/). The Prot-Test server wasutilized to predict models for protein evolution using multiple sequencealignments. Finally, phylogenetic trees were constructed according tothe model of protein evolution for each multiple sequence alignment bythe PhyML 3.0 server. Trees were visualized in the Dendroscope 3program. The TMHMM Server v/2.0 was used for predicting protein membranelocalization.

Purification of Cell-Bound EPS

For EPS purification, the EPS overproducing ΔpdeB/C/D strain (Table 4),which lacks all listerial c-di-GMP PDE genes, pdeB, pdeC, and pdeD, wasused. The ΔpdeB/C/D ΔpssC strain, in which the pssC gene encoding aglycosyltransferase was deleted, is impaired in EPS production and wasused as a negative control. Listerial EPS was purified according toknown procedures with the following modifications. An overnightΔpdeB/C/D BHI culture was transferred to 1 1 of Hsiang-Ning Tsai mediumsupplemented with 3% (wt/v) glucose (HTM/G) (5×200 ml in 21 flasks) atan OD600 of 0.01 and incubated with gentle shaking (125 rpm) at 30° C.for 48 h. Both dispersed cells and aggregates were collected bycentrifugation (5,000 rpm, 15 min, 4° C.) and resuspended in 20 mldeionized water. The cell suspension was boiled for 5 min andcentrifuged (15,000 rpm, 45 min, 4° C.). The supernatant was collectedand precipitated with 4 volumes of cold (4° C.) ethanol overnight at 4°C. After washing the precipitant with water, the sample was treated withlysozyme (4 mg ml⁻¹), mutanolysin (25 μg ml⁻¹), DNase I (0.5 mg ml⁻¹)and RNase A (0.5 mg ml⁻¹) at 37° C. for 24 h. Following enzymaticdigestion, the insoluble fraction was collected by centrifugation,washed with water, and dried at 41° C.

Purification of Extracellular Carbohydrates

Culture supernatants of HTM/G-grown cultures of the ΔpdeB/C/D andΔpdeB/C/D ΔpssC strains were collected and precipitated overnight withcold ethanol. After resuspension, pellets were digested with lysozymeand mutanolysin as described above. The protein and nucleic acidcontaminants were removed from the preparations by trichloroacetic acid(TCA) (20%, final TCA concentration) precipitation. After removal of theinsoluble material by centrifugation (15,000 rpm, 1 h, 4° C.), coldethanol was used to precipitate water-soluble carbohydrates. Theprecipitate was solubilized in deionized water and extensively dialyzedagainst deionized water over 24 h. Carbohydrate samples were lyophilizedand stored at −80° C. prior to NMR analysis.

Total Carbohydrate Content Determination

Total carbohydrates were determined using an anthrone assay. Dried EPSsamples were transferred to 0.4 ml of water and mixed with an ethylacetate solution containing anthrone reagent (2% w/v). Then, 1 ml ofconcentrated sulfuric acid was added to the mixture for colordevelopment. Samples were read at a wavelength of 620 nm, and glucosewas used as a standard to estimate carbohydrate levels in the samples.Finally, dried EPS samples were sent to the Complex CarbohydrateResearch Center for determination of monosaccharide composition,linkage, and NMR analysis.

NMR Spectroscopy of Extracellular Soluble Carbohydrates

Extracellular soluble carbohydrate samples from the ΔpdeB/C/D andΔpdeB/C/D ΔpssC strains were dissolved in 650 μL D₂O (99.9% d). Samplesin H₂O were prepared in a 10% D₂O/90% H₂O mixture to a total volume of650 μL. Reference samples were prepared by dissolving the standardsN-acetyl-D-glucosamine and L-rhamnose in D₂O to final volumes of 650 μLand final concentrations of 50 mM.

NMR spectra were collected at 600 MHz in a BrukerAvance II 600spectrometer with a 5.0 mm multi-nuclear broad-band observe probe. AllNMRspectra were collected at 298 K. Solvent suppression for all sampleswas performed using a pre-saturation sequence incorporated into theone-(1D) and two-dimensional (2D) experiments. 1D spectra were obtainedusing a 12 μs 90° pulse with 32 K data points. 2D total correlationspectroscopy (TOCSY) experiments for samples in D₂O and H₂O wererecorded with an 80 ms mixing time, 512 μl points and 2,048 complexpoints for each free induction decay.

Processing and analysis of the 2D NMR data were performed using NMRPipe,NMRViewJ, and Topspin 3.0 software. Spectra were Fourier transformedusing Lorentzian-to-Gaussian weighting and phase shifted sine-bellwindow functions.

NMR Spectroscopy of Cell Surface-Bound Insoluble EPS

N-deacetylation was performed to obtain soluble EPS material for NMRstudies. The insoluble EPS sample was suspended in 300 μl of 50% NaOHand heated to 80° C. for 1 h. After cooling to room temperature, thesample was diluted with 1 ml of water and acidified with glacial aceticacid (final pH˜4-5). The sample was dialyzed against running deionizedwater for 36 h using a 3,500 Da regenerated cellulose membrane andlyophilized. This material was designated ‘EPS-N’. EPS-N was dissolvedin 5 ml of 0.4 M HCl and heated at 110° C. for 2 h for partialhydrolysis. After cooling to room temperature, the sample was dialyzedtwice against 41 deionized water (6 h and 24 h, respectively) using a1,000 Da regenerated cellulose membrane and then lyophilized. Thismaterial was designated ‘EPS-H’.

To determine 1JCH coupling constants for both α- and β-anomers,mannosamine hydrochloride was synthesized. Briefly, 40 mgN-acetylmannosamine was dissolved in 300 μl 2.4 M HCl and heated in asealed tube for 5 h at 100° C. The mixture was dried with a stream ofnitrogen, dissolved in D₂O, and lyophilized. For NMR, the sample wasdissolved in 700 μl D₂O.

The samples were deuterium exchanged by dissolving in 20 mM DC1 in D₂Oand lyophilization and were subsequently dissolved in 0.27 ml of 20 mMDC1 in D₂O. 1-D proton and 2-D COSY, TOCSY, NOESY, HSQC spectra wereobtained on a Varian Inova-600 MHz spectrometer at 50° C. using standardVarian pulse sequences. The spectral window was from 5.76 to 1.07 ppm(2815 Hz) in the proton dimensions and from 120 to 40 ppm (1263 Hz) inthe carbon dimension. Scan/increment combinations were 4/400 (COSY),8/128 (TOCSY), 400/80 (HSQC) and 16/128 (NOESY) for EPS-N and 8/400(COSY), 16/128 (TOCSY), 128/80 (HSQC) and 16/128 (NOESY) for EPS-H.Mixing times were 80 ms for TOCSY and 300 ms for NOESY.

The HSQC experiment without decoupling during acquisition for thedetermination of 1JCH coupling constants was acquired with a spectralwindow of 110-90 ppm (3,017 Hz) in 16 increments of 256 scans each. Thespectra were processed using the MNova NMR software. Line fitting wasperformed in MNova using a Lorentzian-Gaussian line shape type andsimulated annealing with a maximum number of 500 coarse and 100 fineiterations. Proton chemical shifts were measured relative to an internalacetone standard (δH=2.218 ppm, δC=33.0 ppm).

Phenotypic Assays

Cell aggregation analysis was carried out at 30° C. with gentle shaking(125 rpm) for 48 h in HTM/G using overnight BHI cultures to inoculateHTM/G cultures at an OD600 level of 0.01. The extent of cell aggregationwas also determined by measuring the reduction in OD600 values of HTM/Gcultures standing for 2 min periods. To visualize EPS production by L.monocytogenes strains, overnight BHI cultures were streaked on HTM/Gwith 40 μg/ml Congo red dye and incubated at 30° C. for 48 h.

Scanning Electron Microscopy (SEM)

The EPS overproducer strain ΔpdeB/C/D, the EPS negative strain ΔpdeB/C/DΔpssC, and the wild-type strain EGD-e grown in HTM/G media were mountedon polylysine-treated microscope slides. SEM samples were preparedaccording to known methods with minor modifications. Briefly, cells werefixed with 3% gluteraldehyde and 0.1% ruthenium red in PBS at roomtemperature for 2 h. After washing three times with PBS, cells weredehydrated in 50 ml of a series of 30, 50, 60, 70, 90 and 95% ethanolsolutions for 10 min at each dilution. The dehydration steps werecompleted by immersing slides three times in 100% ethanol for 10 min.Cells were then subjected to critical point drying and immediatelycoated with gold. SEM images of cells were acquired in HV mode using anaccelerating voltage of 20 kV, a spot size of 3, and a working distanceof 11 mm on a Quanta FEG MK2 Scanning Electron Microscope.

Construction of In-Frame Deletion Strains

The EPS synthesis genes pssA, pssB, and pssD in the pssA-E operon, pssZ,a gene encoded within a c-di-GMP signaling module (dgcA-dgcB-pssZ-pdeC),and three DGCs (dgcA, dgcB and dgcC) were deleted in-frame in theΔpdeB/C/D strain using the splice-by-overlap extension PCR method. Two400 bp fragments flanking and overlapping the coding regions at the 5′and 3′ ends of the gene of interest were amplified and combined by PCRamplifications using EGD-e genomic DNA, Pfu Turbo DNA polymerase, andprimers listed, Table 5.

TABLE 5Primers used (SEQ ID NOS 7-46, respectively, in order of appearance)In-frame pssA.PA gggctgcagaatttgttgtaatttgtcgaca deletion pssA.PBttacgcattccgctcaccggatttaactttccttatcat pssA.PC ggtgagcggaatgcgtaapssA.PD gggggatccagaagcatctgtaattgcttt pssB.PAgggctgcagaaactttgaaaaggcgacag pssB.PBatatttcttcatgtaaagccgaatacttataatcatttttttacg pssB.PCcggctttacatgaagaaatat pssB.PD gggggatccgcctgtaatattatcggtatt pssD.PAgggctgcagtaggcgcgttcgctttga pssD.PBgctccggcgatatttacgcagccacattacagtaaattt pssD.PC cgtaaatatcgccggagcpssD.PD gggggatcctttcgtgttttcttcttgaag pssZ.PAgggctgcagaaagaaataaatgattttcatgg pssZ.PBttatttcttaagagttatttattaattaggatgaatcgtttcat pssZ.PCaaagaaataactcttaagaaataa pssZ.PD ggggtcgacaaagaaataaatgattttcatggdgcA.PA gatcac ctgcag ccgtcctgtatctccttcgagtg dgcA.PBgcgaatatgtacttgcgccatgctgttccataatgaatcaag dgcA.PCtggaacagcatggcgcaagtacatattcgcgaaacagaaccag dgcA.PDtcgatagaattcgcagttacaaagaacagcaagaaatactcg dgcB.PAgatcacctgcagcctttgatgctgcattcaaccatg dgcB.PBctgatgaacagcaatattttggaaccaattagggcgatattgtc dgcB.PCaattggttccaaaatattgctgttcatcagggggaac dgcB.PDtcgatagaattctctgttgcattgcttggatatttagatagc dgcC.PAatagatctgcagcggcatctggaatggggcaacaaattgc dgcC.PBtaacgttctagacaactgttcgaccaaaaagcatc dgcC.PCattgcatctagagtatgtattgcagacggaaattagtctg dgcC.PDgtcataggtacccttacctcgccagtttcaagcactcg dgcAB.PAatcgatctgcaggaaattcgctaaaattaagttctagc dgcAB.PBgctctaggatccccataatgaatcaagaatatttggc dgcAB.PCcgagatggatccgaactcgaatgaaacgattcatc dgcAB.PDatctcggaattctacggagggctttttcatttgtc Chromosomal pssZ.FPgggccatggggatgaaacgattcatcctaatt expression pssZ.RPgggctgcagttatttcttaagagttatttctttatt pssZ::E72Q.PAgggccatggggatgaaacgattcatcctaatt pssZ::E72Q.PBcatataaagtccaatgctctgggctagatagtggggttc pssZ::E72Q.PCcagagcattggactttatatg pssZ::E72Q.PD gggctgcagttatttcttaagagttatttctttPssZ and FP ggggctagccgaccagagtctaaaaag PssZ E72Q RPgggaagctttttcttaagagttatttctttatt purification

The resulting 800 bp DNA in-frame deletion fragments and the suicideshuttle vector pKSV7 were digested with PstI and BamHI and ligated withT4 DNA ligase overnight at 18° C. The resulting deletion constructs wereintroduced into and maintained in DH5α and were subsequently transferredto L. monocytogenes strains via electroporation. To insert theconstructs via homologous recombination, four consecutive passages werecarried out at 41° C. in the presence 10 μg ml⁻¹ of chloramphenicol. Toexcise the vector from the chromosome, six to eight passages wereperformed at 30° C. with no antibiotics. Revertants (wild-type ordeletion mutants) were screened for on BHI agar plates supplemented with10 μg ml⁻¹ chloramphenicol. In-frame deletion mutants were identified bycolony PCR analysis of chloramphenicol sensitive clones.

Construction of pssZ Chromosomal Expression Mutants

The pssZ gene was introduced into the ΔpdeB/C/D and ΔpdeB/C/D ΔpssZstrains for overexpression and complementation purposes, respectively. ADNA fragment prepared by PCR amplification encoding pssZ was digestedwith NcoI and BamHI and ligated into the pIMK2 expression vectordigested with the same restriction enzymes. This expression construct,pIMK2-pssZ, was transformed into E. coli S17-1 strain, which was used inconjugation with the L. monocytogenes strains. Briefly, L. monocytogenesstrains (recipients) and S17-1 harboring the expression construct(donor) were grown in BHI and LB with 50 μg ml⁻¹ kanamycin,respectively, overnight at 37° C. Overnight cultures were diluted infresh medium and grown until the OD600 reached 0.5. The donor (2.5 ml)and recipient (1.5 ml) cultures were mixed, centrifuged, washed toeliminate kanamycin, and the final pellets were resuspended in 25 μL BHIand spotted on BHI agar plates. After 24 h of incubation at 30° C., theconjugation mixtures were resuspended in PBS and plated on BHI agarplates supplemented with 100 μg ml⁻¹ nalidixic acid and 50 μg ml⁻¹kanamycin. Transformed strains with the chromosomal expression constructwere observed after 48 h of incubation at 30° C. pIMK2::pssZ::E72Q wasintroduced into L. monocytogenes genomes using the same procedure aspIMK2::pssZ.

Purification of PssZ Proteins

The glycosylhydrolase activity against listerial EPS was tested in vitrousing purified PssZ and PssZ E72Q proteins. Primers were designed toexclude the transmembrane domains from the N-terminal ends of theproteins and add C-terminal His₆-tags (SEQ ID NO: 4) (Table 5). The pssZand pssZ::E72Q genes were cloned into pET23a using NheI and HindIIIsites and transformed into BL21 (DE3) pLysS. The two proteins werepurified by a batch method using Ni-NTA affinity resin from 100 ml of LBmedium supplemented with 100 μg ml⁻¹ ampicillin and 25 μg ml⁻¹chloramphenicol after induction with 0.1 mM IPTG for 3 h at roomtemperature. Following induction, cells were harvested, resuspended in abinding buffer [20 mM sodium phosphate, 0.5 M NaCl and 20 mM imidazole,protease inhibitor cocktail, pH 7.4], and lysed via French Pressdisruption and sonication. Cleared lysates were loaded onto Ni-NTAresin, incubated at 4° C. overnight, washed, and eluted (20 mM sodiumphosphate, 0.5 M NaCl and 250 mM imidazole, pH 7.4). Fractions withrecombinant proteins were desalted with Thermo Scientific Zeba SpinDesalting Columns and concentrated with Amicon Ultra Centrifugal Units(30 kDa cutoff). Final concentrates were filter sterilized using a 0.2μm syringe filter. Final protein preparations were analyzed by sodiumdodecyl sulfate polyacrylamide gel electrophoresis, and concentrationswere determined by a Bio-Rad protein assay using BSA standard.

Glycosylhydrolase Activity Assays

The EPS hydrolytic activities of PssZ and PssZ E72Q were assessed by theability of these proteins: (i) to prevent aggregation of the growingΔpdeB/C/D strain in HTM/G medium, (ii) to disperse nongrowing ΔpdeB/C/Daggregates; and (iii) to release soluble carbohydrates from the purifiedinsoluble EPS fibers. (i) Different concentrations (0.13 and 1.3 μgml⁻¹) of the purified PssZ and PssZ E72Q proteins were added at thebeginning of strain incubation. (ii) Aggregates were washed twice andresuspended in HTM salts-MOPS medium. Proteins were added to 1 ml ofaggregate suspension (32 μg ml⁻¹, final concentration), and samples wereincubated at 30° C. with gentle shaking. The turbidity of the sampleswas used as an indication of cell dispersion. (iii) Purified EPS fiberswere incubated with PssZ or PssZ E72Q at 32 μg ml⁻¹ (finalconcentration). Released soluble carbohydrates were assayed using theanthrone reaction.

Example III

This Example describes methods for identifying and producing PssZhomologs.

Proteins homologous to L. monocytogenes PssZ are present in diversebacteria, including extremophiles capable of living at temperatures from−10° C. to 65° C. Some of these bacteria live at high salinity (up to20% [w/v] NaCl) and alkalinity (up to pH 9). L. monocytogenes PssZ islocated on the outer surface of bacteria where PssZ hydrolyzes Pssexopolysaccharide. The PssZ homologs likely function in a similarmanner, therefore they can be predicted to withstand the pH and salinityof environment. The relatively high percent sequence similarity amongPssZ homologs indicates that the PssZ homologs are suitable forhydrolyzing listerial Pss exopolysaccharide at the temperatures,salinity, and pH in which their hosts can grow. These PssZ proteins cantherefore be used for hydrolyzing listerial EPS-coated aggregates andfor preventing formation of such aggregates in cleaning and washingsolutions at the temperatures ranging from sub-zero to 65° C., salinityfrom 0 to 20% [w/v] NaCl, and alkaline conditions up to pH 9.0 orhigher.

Examples of selected PssZ homologs from representative bacteria withdesirable properties are shown below (as BLAST alignments to PssZ).

1. Exiguobacterium undae, a psychrophile isolated from a lake inAntarctica.

[SEQ ID NO: 47] 1mfmtrqqdpv iqqvetvymk egliraydre eaqrlseslg qymvylleig dadrfaeqvd 61ilrkqflvtt eegdfikwel tpktatnaiv ddfrisnalf aaakrfdepd yqqlsrridd 121givehmkvsg vpidfydwnl kmqtnelrin yldatalkrl nlvepvqevl qaaprsgpff 181heiylpedkr yktaddkevn midqaliaiv seeltgqqde afyafidqem kkgklyaryd 241rstasprsdd esssvyalll pyvseevqrk mterldqidl tdaatthvfd ylneaiarvq 301tsmpnk (referred to herein as Exiguobacterium undae PssZ)>ref|WP_051523998.1| hypothetical protein [Exiguobacterium undae]Length = 306Score = 206 bits (525), Expect = 4e−60, Method: Compositional matrix adjust.Identities = 122/309 (39%), Positives = 186/309 (60%), Gaps = 27/309 (9%)(SEQ ID NOS 48 and 49, respectively, in order of appearance) Query  34KETTPTSTSVQT-YVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQK  92++  P    V+T Y+KE      GLI  Y + EE   L+ES+G YM YL+E+ D+  F + Sbjct   5RQQDPVIQQVETVYMKE------GLIRAY-DREEAQRLSESLGQYMVYLLEIGDADRFAE  57 Query 93 QVNHLEKYFIA---EDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADK 149QV+ L K F+    E +FIKWE T  T TNAIVDDFRI+ AL+ A+++F  P Y++++ + Sbjct  58QVDILRKQFLVTTEEGDFIKWELTPKTATNAIVDDFRISNALFAAAKRFDEPDYQQLSRR 117 Query150 FLTNTKKYSAEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTI---- 205      ++    GVP+DFYD+  K + + L L+YL+  A++++N  +    P+Q + Sbjct 118IDDGIVEHMKVSGVPIDFYDWNLKMQTNELRLNYLDATALKRLNLVE----PVQEVLQAA 173 Query206 -NADPFFTEVF--QNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASK 262  + PFF E++  ++ ++K AD KEVNMIDQ LIAI   +  G  +  F  F+  E+  K Sbjct 174PRSGPFFHEIYLPEDKRYKTADDKEVNMIDQALIAIVSEELTGQQDEAFYAFIDQEM-KK 232 Query263 GKIYARYQRETKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETTHF 322GK+YARY R T  P S++ES++VYA L  Y ++  Q K      E L+++D ++  TTH Sbjct 233GKLYARYDRSTASPRSDDESSSVYALLLPYVSEEVQRK----MTERLDQIDLTDAATTHV 288 Query323 FDYINKEIT 331 FDY+N+ I Sbjct 289 FDYLNEAIA 297

2. Carnobacterium mobile, a psychrophile isolated from Siberianpermafrost.

[SEQ ID NO: 50] 1mnkkrfylil vlillissll alsfhqkigv qevvnnkyen nkgliknyak ngkvqylses 61igqylsylll vedekefkqq vavlkknflv kqadgtfiqw vatnqtttna svddfriiav 121lkkaseqfqe payqiladel eetliskqlt dglivdfydw elqkkaavlh lsyiddqiik 181tdskvnkaky qkilmesvds dtpffkevyt leeqtyqlad kksvnlidql miaiqyvklt 241nqtpaqfdqw lkaewdangk ffggylrtdl tpavpyessa vyalatlyfk lvheeayaeq 301lhqvllkqsp fdknadyati hffdymwvkt vdvlykkdli dk (referred toherein as Carnobacterium mobile PssZ)>ref|WP_051929818.1| hypothetical protein [Carnobacterium mobile]Length = 342Score = 182 bits (463), Expect = 2e−50, Method: Compositional matrix adjust.Identities = 112/298 (38%), Positives = 168/298 (56%), Gaps = 13/298 (4%)(SEQ ID NOS 51 and 52, respectively, in order of appearance) Query  42SVQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYF 101 VQ  V   Y    GLI +Y    +  YL+ESIG Y+ YL+ V D K F++QV  L+K F Sbjct  29GVQEVVNNKYENNKGLIKNYAKNGKVQYLSESIGQYLSYLLLVEDEKEFKQQVAVLKKNF  88 Query102 I---AEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYS 158+   A+  FI+W AT+ TTTNA VDDFRI   L +ASE+F  P+Y+ +AD+ Sbjct  89LVKQADGTFIQWVATNQTTTNASVDDFRIIAVLKKASEQFQEPAYQILADELEETLISKQ 148 Query159 AEQGVPVDFYDFVHKKKADTLHLSYLNIQAMQ---QINYRDKAYLPIQTINAD-PFFTEV 214   G+ VDFYD+  +KKA  LHLSY++ Q ++   ++N      + ++++++D PFF EV Sbjct 149LTDGLIVDFYDWELQKKAAVLHLSYIDDQIIKTDSKVNKAKYQKILMESVDSDTPFFKEV 208 Query215 F--QNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRE 272+  +   ++ AD+K VN+IDQ++IAI Y          FD +L+ E  + GK +  Y R Sbjct 209YTLEEQTYQLADKKSVNLIDQLMIAIQYVKLTNQTPAQFDQWLKAEWDANGKFFGGYLRT 268 Query273 TKKPSSENESTAVYAFLTQYFNKTNQAKNGKITKELLEKMD----TSNPETTHFFDYI 326   P+   ES+AVYA  T YF   ++    +   ++L K       ++  T HFFDY+ Sbjct 269DLTPAVPYESSAVYALATLYFKLVHEEAYAEQLHQVLLKQSPFDKNADYATIHFFDYM 326

3. Carnobacterium jeotgali, a bacterium able to grow at 4-37° C., at pH5.5-9.0 and in the presence of 0-5% (w/v) NaCl.

[SEQ ID NO: 53] 1mskkrffmil lvillitilt llfsynkrev qeviennykn ddnliknyak nnqieylses 61tgqylyylll vkdekefkqq vdslknnfiv krsdgtyikw ttsdqtttna svddfriiev 121lrkggkyfqe pdyvilanel eetlnskqlt dglivdfydw elqkkattvh lsyindqiik 181gnarvdpady qkllagstns qnpffkeiyt vdkhsylsad kntvnmidqf miaiqylkfm 241nqvppefdqw vkqewdtngk lfggyvkstr tpavpyessa vyalaylyfk qaneekyade 301lyamiltqps fdknpdyski hffdyiwiet anaiyktrdk tq (referred toherein as Carnobacterium jeotgali PssZ)>ref|WP_029276582.1| hypothetical protein [Carnobacterium jeotgali]Length = 342Score = 172 bits (435), Expect = 2e−46, Method: Compositional matrix adjust.Identities = 110/301 (37%), Positives = 164/301 (54%), Gaps = 21/301 (7%)(SEQ ID NOS 54 and 55, respectively, in order of appearance) Query  43VQTYVKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFI 102VQ  ++ NY   + LI +Y    +  YL+ES G Y+ YL+ V D K F++QV+ L+  FI Sbjct  30VQEVIENNYKNDDNLIKNYAKNNQIEYLSESTGQYLYYLLLVKDEKEFKQQVDSLKNNFI  89 Query103 ---AEDNFIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSA 159   ++  +IKW  +D TTTNA VDDFRI E L +  + F  P Y  +A++ Sbjct  90VKRSDGTYIKWTTSDQTTTNASVDDFRIIEVLRKGGKYFQEPDYVILANELEETLNSKQL 149 Query160 EQGVPVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKA----YLPIQTINADPFFTEVF 215  G+ VDFYD+  +KKA T+HLSY+N Q ++     D A     L   T + +PFF E++ Sbjct 150TDGLIVDFYDWELQKKATTVHLSYINDQIIKGNARVDPADYQKLLAGSTNSQNPFFKEIY 209 Query216 QNGQFKF--ADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRET 273   +  +  AD+  VNMIDQ +IAI Y      + P FD +++ E  + GK++  Y + T Sbjct 210TVDKHSYLSADKNTVNMIDQFMIAIQYLKFMNQVPPEFDQWVKQEWDTNGKLFGGYVKST 269 Query274 KKPSSENESTAVYAFLTQYFNKTNQAKNGK------ITKELLEKMDTSNPETT--HFFDY 325+ P+   ES+AVYA    YF + N+ K         +T+   +K    NP+ +  HFFDY Sbjct 270RTPAVPYESSAVYALAYLYFKQANEEKYADELYAMILTQPSFDK----NPDYSKIHFFDY 325 Query326 I 326 I Sbjct 326 I 326

4. Jeotgalibacillus campisalis, a halophilic bacterium capable of growthin the presence of 0-20% (w/v) NaCl.

>ref|WP_041061425.1| hypothetical protein [Jeotgalibacillus campisalis]Length = 304Score = 155 bits (393), Expect = 1e−40, Method: Compositional matrix adjust.Identities = 112/290 (39%), Positives = 151/290 (52%), Gaps = 14/290 (5%)[SEQ ID NO: 56] 1mfstdptlqv vkeqytnqeg lihayplqqd seylsesigl ymeylvlvkd eerfseqyei 61lmnnyqiqqg dlifiqwvlk mntkanalid dvriisalhd astlfeepky aesanqltla 121itsnqksngy tvdfydwsln mpakritlsy ltneffqstt dtdnmkdllk nlddttvffp 181eyfdvtkrky reseevhmid qlliainren igypseifkt wclnewkheg kiygrydrqt 241ktasvtyesl avyyylntyf qkinepdlak evlehaella sestigeahf fdyihfqlmk 301knme (referred to herein as Jeotgalibacillus campisalis PssZ)(SEQ ID NOS 57 and 58, respectively, in order of appearance) Query  47VKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHL-EKYFIAED 105VKE YT + GLI  Y   ++  YL+ESIGLYMEYLV V D + F +Q   L   Y I + Sbjct  11VKEQYTNQEGLIHAYPLQQDSEYLSESIGLYMEYLVLVKDEERFSEQYEILMNNYQIQQG  70 Query106 N--FIKWEATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQGV 163+  FI+W    +T  NA++DD RI  AL+ AS  F  P Y + A++            G Sbjct  71DLIFIQWVLKMNTKANALIDDVRIISALHDASTLFEEPKYAESANQLTLAITSNQKSNGY 130 Query164 PVDFYDFVHKKKADTLHLSYLNIQAMQQINYRDKAYLPIQTI-NADPFFTEVFQNGQFKF 222 VDFYD+     A  + LSYL  +  Q     D     ++ + +   FF E F   + K+ Sbjct 131TVDFYDWSLNMPAKRITLSYLTNEFFQSTTDTDNMKDLLKNLDDTTVFFPEYFDVTKRKY 190 Query223 ADQKEVNMIDQMLIAIAYYDEN-GDIEPNFDNFLQTELASKGKIYARYQRETKKPSSENE 281 + +EV+MIDQ+LIAI    EN G     F  +   E   +GKIY RY R+TK  S   E Sbjct 191RESEEVHMIDQLLIAIN--RENIGYPSEIFKTWCLNEWKHEGKIYGRYDRQTKTASVTYE 248 Query282 STAVYAFLTQYFNKTNQAKNGKITKELLEKMDTSNPETT----HFFDYIN 327S AVY +L  YF K N+     + KE+LE  +    E+T    HFFDYI+ Sbjct 249SLAVYYYLNTYFQKINEP---DLAKEVLEHAELLASESTIGEAHFFDYIH 295

5. Bacillus thermotolerans, a thermophilic bacterium capable of growthup to 65° C. and pH 6.0-9.0.

>gb|KKB33529.1| hypothetical protein QY97_03202 [Bacillus thermotolerans]gb|KKB35790.1| hypothetical protein QY95_03280 [Bacillaceae bacterium MTCC8252] Length = 298Score = 108 bits (269), Expect = 2e−23, Method: Compositional matrix adjust.Identities = 84/258 (33%), Positives = 122/258 (47%), Gaps = 30/258 (12%)[SEQ ID NO: 59] 1mqkdteaaws eeefirivhq yymddsgkir sygteeneey llesmglymk wlsghnreee 61vqelrktvqs efayehasdv flswrvegdq qasvnawidd arilsvlgpa dplfnkiadt 121lkkyqvqngl ivdfydweqe aaservvlsy gtreedalrl tsmdrlylea strsdpfype 181fydvkekkfi esdevhmvdq lliaiqleke kgdnhefwqw lvsewekhqa isgrydrnsh 241kgngiesgav ygiaaewall kgeeelaekw khkgfqlvnp kdhqfdhihf fdliwnap(referred to herein as Bacillus thermotolerans PssZ)(SEQ ID NOS 60 and 61, respectively, in order of appearance) Query  47VKENYTAKNGLIMDYKNTEEPHYLAESIGLYMEYLVEVNDSKTFQKQVNHLEKYFI---A 103V + Y   +G I  Y   E   YL ES+GLYM++L   N  +  Q+    ++  F    A Sbjct  18VHQYYMDDSGKIRSYGTEENEEYLLESMGLYMKWLSGHNREEEVQELRKTVQSEFAYEHA  77 Query104 EDNFIKW--EATDSTTTNAIVDDFRITEALYQASEKFSFPSYKKMADKFLTNTKKYSAEQ 161 D F+ W  E     + NA +DD RI   L  A      P + K+AD      KKY  + Sbjct  78SDVFLSWRVEGDQQASVNAWIDDARILSVLGPAD-----PLFNKIADTL----KKYQVQN 128 Query162 GVPVDFYDFVHKKKADTLHLSY-------LNIQAMQQINYRDKAYLPIQTINADPFFTEV 214G+ VDFYD+  +  ++ + LSY       L + +M      D +YL   T  +DPF+ E Sbjct 129GLIVDFYDWEQEAASERVVLSYGTREEDALRLTSM------DRLYLEAST-RSDPFYPEF 181 Query215 FQNGQFKFADQKEVNMIDQMLIAIAYYDENGDIEPNFDNFLQTELASKGKIYARYQRETK 274+   + KF +  EV+M+DQ+LIAI    E GD    F  +L +E      I  RY R + Sbjct 182YDVKEKKFIESDEVHMVDQLLIAIQLEKEKGD-NHEFWQWLVSEWEKHQAISGRYDRNSH 240 Query275 KPSSENESTAVYAFLTQY 292 K +   ES AVY    ++ Sbjct 241KGNG-IESGAVYGIAAEW 257

Example IV

This Example describes methods of producing a PssZ enzyme or apolysaccharide in an isolated and substantially purified form.

In nature, both the polysaccharide and the PssZ enzyme degrading it arebound to a living L. monocytogenes cell surface. In contrast, the PssZenzyme for use in embodiments of the invention is provided withoutviable L. monocytogenes cells, and preferably in a purified form.

In an embodiment, the PssZ coding sequence from L. monocytogenes isexpressed in a host cell, such as E. coli. A feature of embodiments ofthe invention is the expression of the sequences encoding PssZ. As iswell-known in the art, DNA sequences may be expressed by operativelylinking them to an expression control sequence in an appropriateexpression vector and employing that expression vector to transform anappropriate host cell.

A coding sequence is operatively linked to an expression controlsequence when the expression control sequence controls and regulates thetranscription and translation of that coding sequence. The termexpression control sequences refer to DNA sequences that control andregulate the transcription and translation of another DNA sequence(i.e., a coding sequence). Expression control sequences include, but arenot limited to, promoters, enhancers, promoter-associated regulatorysequences, transcription termination and polyadenylation sequences, andtheir positioning and use is well understood by the ordinary skilledartisan. The term “operatively linked” includes having an appropriatestart signal (e.g., ATG) in front of the DNA sequence to be expressed,and maintaining the correct reading frame to permit expression of theDNA sequence under the control of the expression control sequence andproduction of the desired product encoded by the DNA sequence. If a genethat one desires to insert into a recombinant DNA molecule does notcontain an appropriate start signal, such a start signal can be insertedin front of the gene. The combination of the expression controlsequences and the PssZ coding sequence form a PssZ expression cassette.

As used herein, an exogenous or heterologous nucleotide sequence is onewhich is not in nature covalently linked to a particular nucleotidesequence, e.g., an PssZ coding sequence. Examples of exogenousnucleotide sequences include, but are not limited to, plasmid vectorsequences, expression control sequences not naturally associated withparticular PssZ coding sequences, and viral or other vector sequences. Anon-naturally occurring DNA molecule is one which does not occur innature, and it is thus distinguished from a chromosome, for example. Asused herein, a non-naturally occurring DNA molecule comprising asequence encoding an expression product with PssZ activity is one whichcomprises said coding sequence and sequences which are not associatedtherewith in nature.

Similarly, as used herein an exogenous gene is one which does notnaturally occur in a particular recombinant host cell but has beenintroduced in using genetic engineering techniques well known in theart. An exogenous gene as used herein can comprise a PssZ codingsequence expressed under the control of an expression control sequencenot associated in nature with said coding sequence.

A wide variety of host/expression vector combinations may be employed inexpressing the DNA sequences of this invention. Useful expressionvectors, for example, may consist of segments of chromosomal,nonchromosomal, and synthetic DNA sequences. Suitable vectors includederivatives of SV40 and known bacterial plasmids, e.g., Escherichia coliplasmids colE1, pCR1, pBR322, pMB9, and their derivatives, plasmids suchas RP4; phage DNAs, e.g., M13 derivatives, the numerous derivatives ofphage λ, e.g., Agt11, and other phage DNA; yeast plasmids derived fromthe 2μ circle; vectors useful in eukaryotic cells, such as insect ormammalian cells; vectors derived from combinations of plasmids and phageDNAs, such as plasmids that have been modified to employ phage DNA orother expression control sequences; baculovirus derivatives; and thelike. For mammalian cells there are a number of well-known expressionvectors available to the art.

Any of a wide variety of expression control sequences may be used inthese vectors to express the DNA sequences of this invention. Suchuseful expression control sequences include, for example, the early andlate promoters of SV40 or adenovirus for expression in mammalian cells,the lac system, the trp system, the tac or trc system, the majoroperator and promoter regions of phage λ, the control regions of fd coatprotein, the promoter for 3-phosphoglycerate kinase of phosphatase(e.g., pho5), the promoters of the yeast α-mating factors, and othersequences known to control the expression of genes of prokaryotic oreukaryotic cells or their viruses, and various combinations thereof. Theskilled artisan understands which expression control sequences areappropriate to particular vectors and host cells.

A wide variety of host cells are also useful in expressing the DNAsequences of this invention. These hosts may include well-knownprokaryotic and eukaryotic hosts, such as strains of E. coli,Pseudomonas, Bacillus, Streptomyces, fungi such as yeasts, and animalcells, such as Chinese Hamster Ovary (CHO), R1.1, B-W and L-M cells,African Green Monkey kidney cells (e.g., COS 1, COS-7, BSC1, BSC40, andBMT10), insect cells (e.g., Sf9), and human cells and plant cells inculture.

It is understood that not all combinations of vector, expression controlsequence and host cell will function equally well to express the DNAsequences of this invention. However, one skilled in the art will beable to select the proper vector, expression control sequence, and hostcell combination without undue experimentation to accomplish the desiredexpression without departing from the scope of this invention.

In selecting a suitable expression control sequence, a variety offactors will normally be considered. These include, for example, therelative strength of the promoter, its controllability, and itscompatibility with the particular DNA sequence or gene to be expressed,e.g., with regard to potential secondary structure. Suitable hosts willbe selected by consideration of factors including compatibility with thechosen vector, secretion characteristics, ability to fold proteinscorrectly, and fermentation requirements, as well as any toxicity to thehost of the product encoded by the DNA sequences to be expressed, andthe ease of purification of the expression products. The practitionerwill be able to select the appropriate host cells and expressionmechanisms for a particular purpose.

Several strategies are available for the isolation and purification ofrecombinant PssZ after expression in a host system. One method involvesexpressing the proteins in bacterial cells, lysing the cells, andpurifying the protein. Alternatively, one can engineer the DNA sequencesfor secretion from cells. An PssZ protein can be readily engineered tofacilitate purification and/or immobilization to a solid support ofchoice. For example, a stretch of 6-8 histidines can be engineeredthrough polymerase chain reaction or other recombinant DNA technology toallow purification of expressed recombinant protein over anickel-charged nitrilotriacetic acid (NTA) column using commerciallyavailable materials. Other oligopeptide “tags” which can be fused to aprotein of interest by such techniques include, without limitation,strep-tag (Sigma-Genosys, The Woodlands, Tex.), which directs binding tostreptavidin or its derivative streptactin (Sigma-Genosys); aglutathione-S-transferase gene fusion system which directs binding toglutathione coupled to a solid support (Amersham Pharmacia Biotech,Uppsala, Sweden); a calmodulin-binding peptide fusion system whichallows purification using a calmodulin resin (Stratagene, La Jolla,Calif.); a maltose binding protein fusion system allowing binding to anamylose resin (New England Biolabs, Beverly, Mass.); and anoligo-histidine fusion peptide system which allows purification using aNi²⁺-NTA column (Qiagen, Valencia, Calif.).

Hybridization conditions appropriate for detecting various extents ofnucleotide sequence homology between probe and target sequences andtheoretical and practical consideration are given, for example in B. D.Hames and S. J. Higgins (1985) Nucleic Acid Hybridization, IRL Press,Oxford, and in Sambrook et al. (1989). Under particular hybridizationconditions the DNA sequences of this invention will hybridize to otherDNA sequences having sufficient homology, including homologous sequencesfrom different species. It is understood in the art that the stringencyof hybridization conditions is a factor in the degree of homologyrequired for hybridization. The skilled artisan knows how to manipulatethe hybridization conditions so that the stringency of hybridization isat the desired level (high, medium, low). If attempts to identify andisolate the PssZ gene from another Listeria species or strain fail usinghigh stringency conditions, the skilled artisan will understand how todecrease the stringency of the hybridization conditions so that asequence with a lower degree of sequence homology will hybridize to thesequence used as a probe. The choice of the length and sequence of theprobe is readily understood by the skilled artisan.

The DNA sequences of this invention refer to DNA sequences prepared orisolated using recombinant DNA techniques. These include cDNA sequences,sequences isolated using PCR, DNA sequences isolated from their nativegenome, and synthetic DNA sequences. As used herein, this term is notintended to encompass naturally-occurring chromosomes or genomes. Thesesequences can be used to direct recombinant synthesis of PssZ forenzymatic hydrolysis of EPS, especially from L. monocytogenes.

Isolated PssZ enzyme and/or polysaccharide is separated from the cellsand culture medium from which it was produced. Further purification isoptional and within the realm of the skilled artisan. The enzyme sourcecan be a purified or partly purified enzyme or it can be present in acell extract, recombinantly produced, or otherwise.

It is well-known in the biological arts that certain amino acidsubstitutions can be made within a protein without affecting thefunctioning of that protein. Preferably, such substitutions are of aminoacids similar in size and/or charge properties. For example, Dayhoff etal. (1978) in Atlas of Protein Sequence and Structure, Volume 5,Supplement 3, Chapter 22, pages 345-352, which is incorporated byreference herein, provides frequency tables for amino acid substitutionswhich can be employed as a measure of amino acid similarity. Dayhoff etal.'s frequency tables are based on comparisons of amino acid sequencesfor proteins having the same function from a variety of evolutionarilydifferent sources.

It will be a matter of routine experimentation for the ordinary skilledartisan to use the DNA sequence information presented herein to optimizePssZ expression in a particular expression vector and cell line for adesired purpose. A cell line genetically engineered to contain andexpress an PssZ coding sequence is useful for the recombinant expressionof protein products with the characteristic enzymatic activity of thespecifically exemplified enzyme. Any means known to the art can be usedto introduce an expressible PssZ coding sequence into a cell to producea recombinant host cell, i.e., to genetically engineer such arecombinant host cell. Recombinant host cell lines which express highlevels of PssZ are useful as sources for the purification of thisenzyme.

The amino acids which occur in the various amino acid sequences referredto in the specification have their usual three- and one-letterabbreviations routinely used in the art: A, Ala, Alanine; C, Cys,Cysteine; D, Asp, Aspartic Acid; E, Glu, Glutamic Acid; F, Phe,Phenylalanine; G, Gly, Glycine; H, His, Histidine; I, Ile, Isoleucine;K, Lys, Lysine; L, Leu, Leucine; M, Met, Methionine; N, Asn, Asparagine;P, Pro, Proline; Q, Gin, Glutamine; R, Arg, Arginine; S, Ser, Serine; T,Thr, Threonine; V, Val, Valine; W, Try, Tryptophan; Y, Tyr, Tyrosine.

A protein is considered an isolated protein if it is a protein isolatedfrom a host cell in which it is recombinantly produced. It can bepurified or it can simply be free of other proteins and biologicalmaterials with which it is associated in nature.

An isolated nucleic acid is a nucleic acid the structure of which is notidentical to that of any naturally occurring nucleic acid or to that ofany fragment of a naturally occurring genomic nucleic acid spanning morethan three separate genes. The term therefore covers, for example, a DNAwhich has the sequence of part of a naturally occurring genomic DNAmolecule but is not flanked by both of the coding or noncoding sequencesthat flank that part of the molecule in the genome of the organism inwhich it naturally occurs; a nucleic acid incorporated into a vector orinto the genomic DNA of a prokaryote or eukaryote in a manner such thatthe resulting molecule is not identical to any naturally occurringvector or genomic DNA; a separate molecule such as a cDNA, a genomicfragment, a fragment produced by polymerase chain reaction (PCR), or arestriction fragment; and a recombinant nucleotide sequence that is partof a hybrid gene, i.e., a gene encoding a fusion protein. Specificallyexcluded from this definition are nucleic acids present in mixtures ofDNA molecules, transformed or transfected cells, and cell clones, e.g.,as these occur in a DNA library such as a cDNA or genomic DNA library.

In the present context, a promoter is a DNA region which includessequences sufficient to cause transcription of an associated(downstream) sequence. The promoter may be regulated, i.e., notconstitutively acting to cause transcription of the associated sequence.If inducible, there are sequences present which mediate regulation ofexpression so that the associated sequence is transcribed only when aninducer molecule is present in the medium in or on which the organism iscultivated.

One DNA portion or sequence is downstream of a second DNA portion orsequence when it is located 3′ of the second sequence. One DNA portionor sequence is upstream of a second DNA portion or sequence when it islocated 5′ of that sequence.

One DNA molecule or sequence and another are heterologous to another ifthe two are not derived from the same ultimate natural source. Thesequences may be natural sequences, or at least one sequence can bedesigned by man, as in the case of a multiple cloning site region. Thetwo sequences can be derived from two different species or one sequencecan be produced by chemical synthesis provided that the nucleotidesequence of the synthesized portion was not derived from the sameorganism as the other sequence.

An isolated or substantially pure nucleic acid molecule orpolynucleotide is a PssZ-encoding polynucleotide which is substantiallyseparated from other polynucleotide sequences which naturally accompanyit in the L. monocytogenes genome. The term embraces a polynucleotidesequence which has been removed from its naturally occurringenvironment, and includes recombinant or cloned DNA isolates, chemicallysynthesized analogs, and analogs biologically synthesized byheterologous systems.

A polynucleotide is said to encode a polypeptide if, in its native stateor when manipulated by methods known to those skilled in the art, it canbe transcribed and/or translated to produce the polypeptide or afragment thereof. The anti-sense strand of such a polynucleotide is alsosaid to encode the sequence.

A nucleotide sequence is operably linked when it is placed into afunctional relationship with another nucleotide sequence. For instance,a promoter is operably linked to a coding sequence if the promotereffects its transcription or expression. Generally, operably linkedmeans that the sequences being linked are contiguous and, as necessaryto join two protein coding regions, contiguous and in reading frame.However, it is known that certain genetic elements, such as enhancers,may be operably linked even at a distance even if not contiguous.

The term recombinant polynucleotide refers to a polynucleotide which ismade by the combination of two otherwise separated segments of sequenceaccomplished by the artificial manipulation of isolated segments ofpolynucleotides by genetic engineering techniques or by chemicalsynthesis. In so doing one may join together polynucleotide segments ofdesired functions to generate a desired combination of functions.

Polynucleotide probes include an isolated polynucleotide attached to alabel or reporter molecule and may be used to identify and isolate otherPssZ coding sequences, for example, those from others strains of L.monocytogenes. Probes comprising synthetic oligonucleotides or otherpolynucleotides may be derived from naturally occurring or recombinantsingle or double stranded nucleic acids or be chemically synthesized.Polynucleotide probes may be labeled by any of the methods known in theart, e.g., random hexamer labeling, nick translation, or the Klenowfill-in reaction, or with fluors or other detectable moieties.

Large amounts of the polynucleotides may be produced by replication in asuitable host cell. Natural or synthetic DNA fragments coding for aprotein of interest are incorporated into recombinant polynucleotideconstructs, typically DNA constructs, capable of introduction into andreplication in a prokaryotic or eukaryotic cell, especially culturedmammalian cells, wherein protein expression is desired. Usually, theconstruct is suitable for replication in a host cell, such as culturedmammalian cell or a bacterium, but a multicellular eukaryotic host mayalso be appropriate, with or without integration within the genome ofthe host cell. Commonly used prokaryotic hosts include strains ofEscherichia coli, although other prokaryotes, such as Bacillus subtilisor a pseudomonad, may also be used. Eukaryotic host cells includemammalian cells, yeast, filamentous fungi, plant, insect, amphibian, andavian cell lines. Such factors as ease of manipulation, ability toappropriately glycosylate expressed proteins, degree and control ofrecombinant protein expression, ease of purification of expressedproteins away from cellular contaminants, or other factors thatinfluence the choice of the host cell.

Example V

This Example describes materials and methods useful in degradingbiofilms and controlling pathogenic bacteria. Described are uses of aproduced Listeria monocytogenes PssZ protein, homolog, variant, orfragment, in preventing bacterial exopolysaccharide-dependentaggregation, in degrading a biofilm, and in inhibiting biofilm formationon a surface.

Bacterial biofilms are predominantly composed of a polysaccharide matrixwhich may further incorporate proteins, organic and mineral residues,and environmental particulates. An example of steps of forming a biofilmare as follows. A substratum surface is in contact with a liquid and thesurface may be preconditioned by ambient molecules. Cells come incontact with the surface and some are adsorbed. A plurality of cellsattach to the substratum surface and produce exopolysaccarides andquorum sensing may occur with concomitant changes. Nutrients and oxygendiffuse into the biofilm matrix. Cells in the matrix replicate and grow.The cells continue to produce exopolysaccarides. As the biofilm grows,fragments may detach and be sloughed. The fragments carrying cellsembedded in the matrix may be carried in the liquid to a new location toform a biofilm on another surface.

To control contamination and combat biofilms in food production, such asin the dairy industry, cleaning-in-place (CIP) procedures are usuallyemployed in equipment for processing lines. The basic sequence ofoperations is: 1. a pre-rinse with cold water to remove gross residues;2. a circulation of detergent to remove remaining minor residues; 3. anintermediate cold water rinse to flush out detergent; 4. a circulationof disinfectant to inactivate and kill any residual microorganisms; 5. afinal cold water rinse to flush out detergent. The steps may includeelevated temperatures and acidic or caustic solutions, for example:water rinse, 1% sodium hydroxide at 70 C for 10 min, water rinse, 0.8%nitric acid at 70° C. for 10 min, water rinse, followed by exposure tochlorine or combinations of nisin, lauricidin, and lactoperoxidase.

Addition of the PssZ enzyme at one or more rinse or detergent steps aidsin degrading or digesting biofilms to make the biofilms more susceptibleto cleaning and sanitizing agents. In an embodiment, a cleaning processcomprises PssZ application followed by, or used in conjunction with, oneor more of: water, hydrogen peroxide, alcohol, iodophor, quaternaryammonia compounds, chlorine solutions, peracetic acid, peroctanoic acid,nitric acid, benzoic acid, sodium hydroxide, dimethyl benzyl laurylammonium bromide, cationic surfactants, anionic surfactants, non-ionicsurfactants, zwitterionic surfactants, nisin, lauricidin,lactoperoxidase, ampicillin, vancomycin, ciprofloxacin, azithromycin, ora proteolytic enzyme.

In an embodiment, the PssZ enzyme has at least 90 percent identity toListeria monocytogenes PssZ [SEQ ID NO 1] or 90 percent identity to theL. monocytogenes PssZ protein lacking the transmembrane domain [SEQ IDNO 2]. In an embodiment, the PssZ enzyme has at least 90 percentidentity to a PssZ homolog derived from at least one extremophiledescribed in Example III [SEQ ID NOs 47, 50, 53, 56, 59]. In otherembodiments, the PssZ enzyme has at least 80% identity to to L.monocytogenes PssZ [SEQ ID NO 1], L. monocytogenes PssZ protein lackingthe transmembrane domain [SEQ ID NO 2], or a PssZ homolog derived fromat least one extremophile described in Example III. In otherembodiments, the PssZ enzyme has at least 70% identity to to L.monocytogenes PssZ [SEQ ID NO 1], L. monocytogenes PssZ protein lackingthe transmembrane domain [SEQ ID NO 3], or a PssZ homolog derived fromat least one extremophile described in Example III. In otherembodiments, the PssZ enzyme has at least 60% identity to to L.monocytogenes PssZ [SEQ ID NO 1], L. monocytogenes PssZ protein lackingthe transmembrane domain [SEQ ID NO 2], or a PssZ homolog derived fromat least one extremophile described in Example III. In otherembodiments, the PssZ enzyme is a PssZ homolog, or fragment thereof,identified using BLAST alignment to a known PssZ sequence.

In an embodiment, the temperature of a PssZ solution is maintained at atemperature ranging from about 0° C. to about 65° C. In an embodiment,the pH of a PssZ solution ranges from about 4.0 to about 10.0. In anembodiment, the concentration of a PssZ enzyme in a PssZ solution rangesfrom about 0.1 nM to about 500 mM, or from about 1 nM to about 100 mM,or from about 0.1 mM to about 50 mM. In an embodiment of a method ofcleaning, a PssZ contact time with a surface to be cleaned ranges fromabout 5 seconds to about 1 hour, or from about 30 seconds to about 30minutes, or from about 60 minute to about 2 days.

In an embodiment of the invention, a PssZ application is used toprevent, degrade, or mitigate biofilms on equipment or in a facility. Inan embodiment, the equipment is selected from: conveyers, slicers,peelers, sorters, packaging equipment, milking equipment, vats, tanks,condensing units, drip pans, utensils, sponges, and cleaning brushes. Inan embodiment, facility application of PssZ is made to one or more of:floors, walls, ceilings, sink drains, tables, countertops, food contactsurfaces, air filters, boot baths, floor trenches, and floor drains.

In some embodiments, the PssZ enzyme is stabilized. In some embodiments,a stabilized enzyme solution or compound comprises boric acid, propyleneglycol, phenylboronic acid, glycerol. In some embodiments, the PssZenzyme is stabilized by adsorbtion, covalent binding, crosslinking,entrapment, reversed micelleation, chemical modification,lyophilization, protein engineering, propanol rinsed preparation, ionicliquid coating, or stabilizing additives.

In an embodiment, a purified PssZ enzyme is applied directly to a foodproduct. Listeriosis is of particular concern in ready-to-eatrefrigerated foods because L. monocytogenes can grow at cooltemperatures. An example for application includes rinsing or soakingfood products, such as leafy greens, melons, or fresh cheeses in anaqueous solution containing PssZ. In another example, the foods aresprayed with a solution or aerosol containing purified PssZ. In anotherexample, PssZ is incorporated into a food wax, emulsifier, sausagecasing, waxed carton, or packaging. PssZ may be consumed by humans oranimals with no anticipated adverse impact.

In an embodiment, a purified PssZ enzyme is applied directly to animalsilage. In an embodiment, the application is performed prior tolong-term storage of the silage.

In an embodiment, a non-pathogenic Listeria species is engineered toexpress the PssZ enzyme. Listeria species selected may include: L.fleischmannii, L. grayi, L. innocua, L. marthii, L. rocourtiae, L.seeligeri, L. weihenstephanensis, or L. welshimeri. In an embodiment,the produced enzyme is harvested. In another embodiment, the engineeredListeria sp. is inoculated into a system where it competes with thepathogenic L. monocytogenes and/or L. ivanovii and aids in thedegradation of biofilms.

It is understood that even though the E72Q mutant is less catalyticallyactive than certain other PssZ proteins, fragments, or variants, theE72Q mutant can nonetheless be used in any of the embodiments describedherein.

Example VI

This Example describes uses of a polysaccharide having the compositionof a trisaccharide repeating unit of{4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, wherein ManpNAc isN-acetylmannosamine and Galp is galactose. The resistance of thelisterial polysaccharide to dessication and chemical degradation isevident from the persistent challenges in controlling listerialcontamination. These same characteristics, in conjunction with thedisclosed methods for degrading the polysaccharide, provideopportunities for controlled utilization of a polysaccharide matrix.

The present disclosure, providing the structure of the polysaccharide,further provides an edible compound. In an embodiment, thepolysaccharide is used as an encapsulating compound for transportingparticulates or probiotics to the intestine. In another embodiment, thepolysaccharide is used as a food additive or filler. As one non-limitingexample, the polysaccharide can be used in ice cream or other emulsionto prevent the product from developing frost crystals.

Example VII

Embodiments of the present disclosure can be formulated as part of a kitor kits. A non-limiting example of such a kit is a kit for amelioratinga bacterial contamination, which includes a PssZ enzyme solution and adisinfectant solution in separate containers, where the containers mayor may not be present in a combined configuration. Many other kits arepossible. The kits may further include instructions for using thecomponents of the kit to practice the subject methods. The instructionsfor practicing the subject methods are generally recorded on a suitablerecording medium. For example, the instructions may be present in thekits as a package insert or in the labeling of the container of the kitor components thereof. In other embodiments, the instructions arepresent as an electronic storage data file present on a suitablecomputer readable storage medium, such as a flash drive, CD-ROM, ordiskette. In other embodiments, the actual instructions are not presentin the kit, but means for obtaining the instructions from a remotesource, such as via the internet, are provided. An example of thisembodiment is a kit that includes a web address where the instructionscan be viewed and/or from which the instructions can be downloaded. Aswith the instructions, this means for obtaining the instructions isrecorded on a suitable substrate.

Certain embodiments of the compositions and methods disclosed herein aredefined in the above examples. It should be understood that theseexamples, while indicating particular embodiments of the invention, aregiven by way of illustration only. From the above discussion and theseexamples, one skilled in the art can ascertain the essentialcharacteristics of this disclosure, and without departing from thespirit and scope thereof, can make various changes and modifications toadapt the compositions and methods described herein to various usagesand conditions. Various changes may be made and equivalents may besubstituted for elements thereof without departing from the essentialscope of the disclosure. In addition, many modifications may be made toadapt a particular situation or material to the teachings of thedisclosure without departing from the essential scope thereof.

What is claimed is:
 1. A cleaning solution comprising: an enzyme,wherein the enzyme is a produced PssZ protein modified to lack atransmembrane domain, and wherein the enzyme has functional activity tohydrolyze an exopolysaccharide produced by Listeria monocytogenes; and adisinfectant, a surfactant, a second enzyme, or an anti-bacterial agent.2. The cleaning solution of claim 1: wherein the produced PssZ proteinhas functional activity to hydrolyze a ManNAc-Gal exopolysaccharidehaving a trisaccharide repeating unit of{4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, wherein ManpNAc isN-acetylmannosamine and Galp is galactose.
 3. The cleaning solution ofclaim 1, wherein the produced PssZ protein has at least 70% amino acidsequence identity to a Listeria monocytogenes PssZ protein.
 4. Thecleaning solution of claim 1, wherein the produced PssZ protein has atleast 33% amino acid sequence identity to a Listeria monocytogenes PssZprotein.
 5. The cleaning solution of claim 1, wherein the produced PssZprotein has at least 60% amino acid sequence identity to a sequenceselected from the group consisting of: SEQ ID NO: 2, SEQ ID NO: 47, SEQID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, and SEQ ID NO:
 59. 6. Thecleaning solution of claim 1, wherein the disinfectant, surfactant,second enzyme, or anti-bacterial agent is selected from the groupconsisting of: sodium hypochlorite, hydrogen peroxide, benzalkoniumchloride, alcohol, iodophor, quaternary ammonia compounds, chlorinesolutions, peracetic acid, peroctanoic acid, nitric acid, benzoic acid,sodium hydroxide, dimethyl benzyl lauryl ammonium bromide, cationicsurfactants, anionic surfactants, non-ionic surfactants, zwitterionicsurfactants, nisin, lauricidin, lactoperoxidase, ampicillin, vancomycin,ciprofloxacin, azithromycin, or a proteolytic enzyme.
 7. The cleaningsolution of claim 1, wherein the cleaning solution has a pH in a rangefrom about 4 to about
 10. 8. The cleaning solution of claim 1, wherein aconcentration of the produced PssZ protein in the cleaning solutionranges from about 0.1 nM to about 500 mM.
 9. A composition forinhibiting aggregation of L. monocytogenes, comprising: an enzyme,wherein the enzyme is a produced PssZ protein modified to lack atransmembrane domain, and wherein the enzyme has functional activity tohydrolyze a listerial Pss exopolysaccharide comprising a trisacchariderepeating unit of {4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-},wherein ManpNAc is N-acetylmannosamine and Galp is galactose; andwherein the enzyme is stabilized by adsorbtion, covalent binding,crosslinking, entrapment, reverse micelleation, chemical modification,lyophilization, protein engineering, propanol rinse preparation, ionicliquid coating, or stabilizing additives.
 10. The composition of claim9, wherein the composition forms a stabilized enzyme solution orcompound comprising boric acid, propylene glycol, phenylboronic acid, orglycerol.
 11. A method for detecting a listerial biofilm on a surfacecomprising: providing a fusion protein comprising a modified PssZ enzymelacking a transmembrane domain, wherein the modified PssZ enzyme: hasfunctional activity to bind to an exopolysaccharide, produced byListeria monocytogenes, comprising a ManNAc-Gal exopolysaccharide havinga trisaccharide repeating unit of{4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, wherein ManpNAc isN-acetylmannosamine and Galp is galactose, and contacting the surfacewith the fusion protein, whereby the modified PssZ enzyme binds to thelisterial exopolysaccharide comprising the listerial biofilm.
 12. Themethod of claim 11, wherein the modified PssZ enzyme has impairedhydrolytic activity for degrading the listerial Pss exopolysaccharide.13. The method of claim 11, wherein the modified PssZ enzyme is derivedfrom a PssZ E72Q mutant.
 14. The method of claim 11, wherein themodified PssZ enzyme has at least 60% amino acid sequence identity to asequence selected from the group consisting of: SEQ ID NO: 2, SEQ ID NO:47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, and SEQ ID NO:
 59. 15.The method of claim 11, further comprising: hydrolyzing the listerialPss exopolysaccharide, thereby releasing soluble carbohydrates; anddetecting soluble carbohydrates in a solution in contact with thesurface.
 16. The method of claim 11, further comprising: hydrolyzing thelisterial Pss exopolysaccharide, thereby dispersing the listerialbiofilm; and measuring turbidity in a solution in contact with thesurface.
 17. The cleaning solution of claim 1, wherein the enzyme isstabilized by adsorbtion, covalent binding, crosslinking, entrapment,reverse micelleation, chemical modification, lyophilization, proteinengineering, propanol rinsed preparation, ionic liquid coating, orstabilizing additives.
 18. The cleaning solution of claim 1, wherein theenzyme comprises a fusion protein, wherein the produced PssZ proteinfurther comprises a poly-histidine tag.
 19. The cleaning solution ofclaim 1, wherein the enzyme comprises a C-terminal fusion protein,wherein the produced PssZ protein further comprises a poly-histidine taghaving at least 80% sequence identity to SEQ ID NO: 4.